U.S. patent application number 15/630751 was filed with the patent office on 2018-01-11 for methods for identifying, diagnosing, and predicting survival of lymphomas.
This patent application is currently assigned to The United States of America, as represented by he Secretary, Department of Health and Human Servi. The applicant listed for this patent is Board of Regents of the University of Nebraska, British Columbia Cancer Agency Branch, Fundacio Clinic, Hospital Clinic de Barcelona, Julius-Maximilians-University of Wurzburg, Oslo University Hospital HF, Queen Mary and Westfield College, University of London, The United States of America, as represented by the Secretary, Department of Health and Human Serv, The United States of America, as represented by the Secretary, Department of Health and Human Serv, Universitat de Barcelona, University of Arizona, Tech Transfer Arizona, University of Rochester. Invention is credited to James Armitage, Silvia M. Bea, Elias Campo Guerri, Wing C. Chan, Joseph Connors, Sandeep Dave, Jan Delabie, Richard I. Fisher, Kai Fu, Randy Gascoyne, Timothy C. Greiner, Thomas Grogan, Harald Holte, Elaine S. Jaffe, Stein Kvaloy, T. Andrew Lister, Armando Lopez-Guillermo, Thomas Miller, Emilio Montserrat, Victor Moreno, Hans-Konrad Muller-Hermelink, German Ott, John I. Powell, Lisa M. Rimsza, Andreas Rosenwald, Itziar Salaverria, Erlend B. Smeland, Louis M. Staudt, Bruce Tan, Julie Vose, Dennis Weisenburger, Wyndham Wilson, George Wright, Andreas Zetti.
Application Number | 20180011106 15/630751 |
Document ID | / |
Family ID | 38982084 |
Filed Date | 2018-01-11 |
United States Patent
Application |
20180011106 |
Kind Code |
A1 |
Staudt; Louis M. ; et
al. |
January 11, 2018 |
METHODS FOR IDENTIFYING, DIAGNOSING, AND PREDICTING SURVIVAL OF
LYMPHOMAS
Abstract
Gene expression data provides a basis for more accurate
identification and diagnosis of lymphoproliferative disorders. In
addition, gene expression data can be used to develop more accurate
predictors of survival. The present invention discloses methods for
identifying, diagnosing, and predicting survival in a lymphoma or
lymphoproliferative disorder on the basis of gene expression
patterns. The invention discloses a novel microarray, the Lymph Dx
microarray, for obtaining gene expression data from a lymphoma
sample. The invention also discloses a variety of methods for
utilizing lymphoma gene expression data to determine the identity
of a particular lymphoma and to predict survival in a subject
diagnosed with a particular lymphoma. This information will be
useful in developing the therapeutic approach to be used with a
particular subject.
Inventors: |
Staudt; Louis M.; (Bethesda,
MD) ; Wright; George; (Rockville, MD) ; Dave;
Sandeep; (Chapel Hill, NC) ; Tan; Bruce;
(Chicago, IL) ; Powell; John I.; (Ijamsville,
MD) ; Wilson; Wyndham; (Washington, DC) ;
Jaffe; Elaine S.; (Great Falls, VA) ; Chan; Wing
C.; (Pasadena, CA) ; Greiner; Timothy C.;
(Council Bluffs, IA) ; Weisenburger; Dennis;
(Glendora, CA) ; Armitage; James; (Omaha, NE)
; Fu; Kai; (Omaha, NE) ; Fisher; Richard I.;
(Pittsford, NY) ; Rimsza; Lisa M.; (Scottsdale,
AZ) ; Miller; Thomas; (Tucson, AZ) ; Grogan;
Thomas; (Tucson, AZ) ; Campo Guerri; Elias;
(Barcelona, ES) ; Bea; Silvia M.; (Sabadell,
ES) ; Salaverria; Itziar; (Barcelona, ES) ;
Lopez-Guillermo; Armando; (Barcelona, ES) ;
Montserrat; Emilio; (Barcelona, ES) ; Moreno;
Victor; (Barcelona, ES) ; Zetti; Andreas;
(Wurzburg, DE) ; Ott; German;
(Bietigheim-Bissingen, DE) ; Muller-Hermelink;
Hans-Konrad; (Wurzburg, DE) ; Rosenwald; Andreas;
(Wurzburg, DE) ; Vose; Julie; (Omaha, NE) ;
Gascoyne; Randy; (North Vancouver, CA) ; Connors;
Joseph; (Vancouver, CA) ; Smeland; Erlend B.;
(Oslo, NO) ; Kvaloy; Stein; (Oslo, NO) ;
Holte; Harald; (Oslo, NO) ; Delabie; Jan;
(Toronto, CA) ; Lister; T. Andrew; (London,
GB) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
The United States of America, as represented by the Secretary,
Department of Health and Human Serv
Board of Regents of the University of Nebraska
University of Rochester
University of Arizona, Tech Transfer Arizona
Universitat de Barcelona
Fundacio Clinic
Hospital Clinic de Barcelona
Julius-Maximilians-University of Wurzburg
British Columbia Cancer Agency Branch
Oslo University Hospital HF
Queen Mary and Westfield College, University of London |
Bethesda
Lincoln
Rochester
Tucson
Barcelona
Barcelona
Barcelona
Wurzburg
Vancouver
Oslo
London |
MD
NE
NY
AZ |
US
US
US
US
ES
ES
ES
DE
CA
NO
GB |
|
|
Assignee: |
The United States of America, as
represented by he Secretary, Department of Health and Human
Servi
Bethesda
MD
Board of Regents of the University of Nebraska
Lincoln
NE
University of Rochester
Rochester
NY
Arizona Board of Regents on Behalf of the University of
Arizona
Tucson
AZ
Universitat de Barcelona
Barcelona
Fundacio Clinic
Barcelona
Hospital Clinic de Barcelona
Barcelona
Julius-Maximilians-University of Wurzburg
Wurzburg
British Columbia Cancer Agency Branch
Vancouver
Oslo University Hospital HF
Oslo
Queen Mary and Westfield College, University of London
London
|
Family ID: |
38982084 |
Appl. No.: |
15/630751 |
Filed: |
June 22, 2017 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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13409416 |
Mar 1, 2012 |
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15630751 |
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11493387 |
Jul 25, 2006 |
8131475 |
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13409416 |
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10934930 |
Sep 3, 2004 |
7711492 |
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11493387 |
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60500377 |
Sep 3, 2003 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
Y02A 90/26 20180101;
C12Q 2600/112 20130101; G16B 25/00 20190201; C12Q 1/6886 20130101;
Y02A 90/10 20180101; G16B 40/00 20190201; C12Q 2600/118 20130101;
G01N 33/6842 20130101; G01N 2333/51 20130101; C12Q 2600/158
20130101 |
International
Class: |
G01N 33/68 20060101
G01N033/68; G06F 19/20 20110101 G06F019/20; C12Q 1/68 20060101
C12Q001/68 |
Goverment Interests
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH AND
DEVELOPMENT
[0002] This invention was made with government support under Grant
No. U01 CA084967, awarded by NIH. The government has certain rights
in the invention.
Claims
1.-11. (canceled)
12. A method for treating a diffuse large B cell lymphoma (DLBCL)
in a subject comprising: (a) isolating gene expression product from
a DLBCL biopsy sample from a subject with DLBCL; (b) determining an
average gene expression level of genes set forth in Table 2371 for
the proliferation gene expression signature to obtain a
proliferation gene expression signature value; (c) determining an
average gene expression level of genes set forth in Table 2371 for
the germinal center B cell gene expression signature to obtain a
germinal center B cell gene expression signature value; (d)
determining an average gene expression level of genes set forth in
Table 2371 for the MHC class II gene expression signature to obtain
an MHC class II gene expression signature value; (e) determining an
average gene expression level of genes set forth in Table 2371 for
the lymph node gene expression signature to obtain a lymph node
gene expression signature value; (f) measuring the expression level
of BMP6 to obtain a BMP6 expression value; (g) determining a
survival predictor score calculated as [0.241* (proliferation gene
expression signature value)]+[0.310*(BMP6 expression
value)]--[0.290*(germinal center B cell gene expression signature
value)]-[0.311*(MHC class II gene expression signature
value)]-[0.249*(lymph node gene expression signature value)],
wherein a higher survival predictor score indicates worse survival,
and a survival predictor score indicating a 5-year survival rate of
73% or less is calculated; (h) performing comparative genomic
hybridization on a DLBCL biopsy sample from the subject to analyze
for a gain or amplification in the 3p11-p12 region of chromosome 3,
wherein a gain or amplification in said region is detected and
indicates worse survival; and (i) administering cyclophosphamide,
doxorubicine, vincristine, and prednisone to the subject to treat
DLBCL in the subject.
13. The method of claim 12, wherein said subpart (i) of analyzing
for a gain or amplification in the 3p11-p12 region of chromosome 3
further comprises using polymerase chain reaction (PCR).
14. The method of claim 13, wherein the PCR is real-time
quantitative PCR.
15. The method of claim 12, wherein said subpart (i) of analyzing
for a gain or amplification in the 3p11-p12 region of chromosome 3
further comprises using cytogenetic analysis of bands in the
3p11-p12 region of chromosome 3.
16. A method for treating a diffuse large B cell lymphoma (DLBCL)
in a subject comprising: (a) isolating gene expression product from
a DLBCL biopsy sample from a subject with DLBCL; (b) determining an
average gene expression level of genes set forth in Table 2371 for
the proliferation gene expression signature to obtain a
proliferation gene expression signature value; (c) determining an
average gene expression level of genes set forth in Table 2371 for
the germinal center B cell gene expression signature to obtain a
germinal center B cell gene expression signature value; (d)
determining an average gene expression level of genes set forth in
Table 2371 for the MHC class II gene expression signature to obtain
an MHC class II gene expression signature value; (e) determining an
average gene expression level of genes set forth in Table 2371 for
the lymph node gene expression signature to obtain a lymph node
gene expression signature value; (f) measuring the expression level
of BMP6 to obtain a BMP6 expression value; (g) determining a
survival predictor score calculated as [0.241*(proliferation gene
expression signature value)]+[0.310*(BMP6 expression
value)]-[0.290*(germinal center B cell gene expression signature
value)]-[0.311*(MHC class II gene expression signature
value)]-[0.249*(lymph node gene expression signature value)],
wherein a higher survival predictor score indicates worse survival,
and a survival predictor score indicating a 5-year survival rate of
73% or less is calculated; (h) performing cytogenetic analysis of
bands in the 3p11-p12 region of chromosome 3 on a DLBCL biopsy
sample from the subject to analyze for a gain or amplification in
the 3p11-p12 region of chromosome 3, wherein a gain or
amplification in said region is detected and indicates worse
survival; and (i) administering cyclophosphamide, doxorubicine,
vincristine, and prednisone to the subject to treat DLBCL in the
subject.
17. A method for treating a diffuse large B cell lymphoma (DLBCL)
in a subject comprising: (a) isolating gene expression product from
a DLBCL biopsy sample from a subject with DLBCL; (b) determining an
average gene expression level of genes set forth in Table 2371 for
the proliferation gene expression signature to obtain a
proliferation gene expression signature value; (c) determining an
average gene expression level of genes set forth in Table 2371 for
the germinal center B cell gene expression signature to obtain a
germinal center B cell gene expression signature value; (d)
determining an average gene expression level of genes set forth in
Table 2371 for the MHC class II gene expression signature to obtain
an MHC class II gene expression signature value; (e) determining an
average gene expression level of genes set forth in Table 2371 for
the lymph node gene expression signature to obtain a lymph node
gene expression signature value; (f) measuring the expression level
of BMP6 to obtain a BMP6 expression value; (g) determining a
survival predictor score calculated as [0.241* (proliferation gene
expression signature value)]+[0.310*(BMP6 expression
value)]-[0.290*(germinal center B cell gene expression signature
value)]-0.311*(MHC class II gene expression signature
value)]-[0.249*(lymph node gene expression signature value)],
wherein a higher survival predictor score indicates worse survival,
and a survival predictor score indicating a 5-year survival rate of
73% or less is calculated; (h) performing polymerase chain reaction
(PCR) on a DLBCL biopsy sample from the subject to analyze for a
gain or amplification in the 3p11-p12 region of chromosome 3,
wherein a gain or amplification in said region is detected and
indicates worse survival; and (i) administering cyclophosphamide,
doxorubicine, vincristine, and prednisone to the subject to treat
DLBCL in the subject.
18. The method of claim 17, wherein the PCR is real-time
quantitative PCR.
Description
RELATED APPLICATIONS
[0001] The present utility application is a continuation of U.S.
patent application Ser. No. 13/409,416, filed Mar. 1, 2012, which
is a divisional of U.S. patent application Ser. No. 11/493,387,
filed Jul. 25, 2006 (now U.S. Pat. No. 8,131,475), which is a
continuation-in-part of U.S. application Ser. No. 10/934,930
(Staudt et al.), filed Sep. 3, 2004 (now U.S. Pat. No. 7,711,492),
which claims priority to provisional patent application U.S. Ser.
No. 60/500,377, filed Sep. 3, 2003, the disclosures of which are
both incorporated by reference herein in their entirety, including
but not limited to the electronic data submitted on 21 CD-ROMs
accompanying the provisional application.
REFERENCE TO TABLES SUBMITTED ON COMPACT DISC
[0003] Tables 2-1723 and 1725-2358 are contained on 21 CD-ROMs
provided herewith. These CD-ROMs are numbered 1-21 of 22. Each
CD-ROM is provided in two copies, for a total of 44 CD-ROMs. The
name, size, and date of creation for each file is presented in the
file entitled 'Table_of_contents.txt," located on CD number 21 of
22. The name of each file incorporates the number of the
corresponding table. Any reference to a table or file should be
considered an incorporation by reference of the contents of the
table and/or file at that particular place in the
specification.
REFERENCE TO COMPUTER PROGRAM LISTING APPENDIX SUBMITTED ON COMPACT
DISC
[0004] A computer program listing appendix is contained on one
CD-ROM provided herewith. Three copies of this CD-ROM, numbered 22
of 22, are provided. The computer program listing appendix contains
files related to the implementation of an algorithm for determining
lymphoma type. The name, size, and date of creation for each file
in the computer program listing appendix is presented in the file
entitled "Table_of_contents.txt," located on CD-ROM 22. Any
reference to a file contained in the computer program listing
appendix should be considered an incorporation by reference of the
contents of that file at that particular place in the
specification.
BACKGROUND
[0005] A variety of systems for identifying and classifying
lymphomas have been proposed over the last 20 years. In the 1980's,
the Working Formulation was introduced as a method of classifying
lymphomas based on morphological and clinical characteristics. In
the 1990's, the Revised European-American Lymphoma (REAL) system
was introduced in an attempt to take into account immunophenotypic
and genetic characteristics in classifying lymphomas (Harris 1994).
The most recent standard, set forth by the World Health
Organization (WHO), attempts to build on these previous systems
(Jaffe 2001). The WHO classification of lymphomas is based on
several factors, including tumor morphology, immunophenotype,
recurrent genetic abnormalities, and clinical features. Table 1,
below, contains a list of the B and T cell neoplasms that have been
recognized by the WHO classification. Each malignancy is listed
according to its WHO classification nomenclature, followed by a WHO
classification number.
TABLE-US-00001 TABLE 1 Category Name WHO ID # B-cell neoplasms
Precursor B-cell Precursor B-cell lymphoblastic 9835/3 neoplasms
leukemia Precursor B-cell lymphoblastic 9728/3 lymphoma Mature
B-cell Chronic lymphocytic leukemia 9823/3 neoplasms Small
lymphocytic lymphoma 9670/3 B-cell prolymphocytic leukemia 9833/3
Lymphoplasmacytic lymphoma 9671/3 Splenic marginal zone 9689/3
lymphoma Hairy cell leukemia 9940/3 Plasma cell myeloma 9732/3
Solitary plasmacytoma of bone 9731/3 Extraosseous plasmacytoma
9734/3 Extranodal marginal zone B-cell 9699/3 lymphoma of mucosa-
associated lymphoid tissue (MALT lymphoma) Nodal marginal zone
B-cell 9699/3 lymphoma Follicular lymphoma (Grade 1, 9690/3 2, 3a,
3b) Mantle cell lymphoma 9673/3 Diffuse large B-cell lymphoma
9680/3 Mediastinal (thymio) large B-cell 9679/3 lymphoma
Intravascular large B-cell 9680/3 lymphoma Primary effusion
lymphoma 9678/3 Burkitt lymphoma 9687/3 Burkitt leukemia 9826/3
B-cell proliferations of Lymphomatoid granulomatosis 9766/1
uncertain malignant potential Post-transplant 9970/1
lymphoproliferative disorder, polymorphic T-cell and NK-cell
neoplasms Precursor T-cell and Precursor T lymphoblastic 9837/3
NK-cell neoplasms leukemia Precursor T lymphoblastic 9729/3
lymphoma Blastic NK-cell lymphoma 9727/3 Mature T-cell and T-cell
prolymphocytic leukemia 9834/3 NK-cell neoplasms T-cell large
granular 9831/3 lymphocytic leukemia Aggressive NK-cell leukemia
9948/3 Adult T-cell leukemia/lymphoma 9827/3 Extranodal NK-/T-cell
9719/3 lymphoma, nasal type Enteropathy-type T-cell 9717/3 lymphoma
Hepatosplenic T-cell lymphoma 9716/3 Subcutaneous panniculitis-like
9708/3 T-cell lymphoma Mycosis fungoides 9700/3 Sezary syndrome
(9701/3) 9701/3 Primary cutaneous anaplastic 9718/3 large cell
lymphoma (C-ALCL) Peripheral T-cell lymphoma, 9702/3 unspecified
Angioimmunoblastic T-cell 9705/3 lymphoma Anaplastic large cell
lymphoma 9714/3 T-cell proliferation of Lymphomatoid papulosis
9718/3 uncertain malignant potential Hodgkin lymphoma Nodular
lymphocyte 9659/3 predominant Hodgkin lymphoma Classical Hodgkin
lymphoma 9650/3 Classical Hodgkin lymphoma, 9663/3 nodular
sclerosis Classical Hodgkin lymphoma, 9651/3 lymphocyte-rich
Classical Hodgkin lymphoma, 9652/3 mixed cellularity Classical
Hodgkin lymphoma, 9653/3 lymphocyte depleted
[0006] Other diagnoses that have not been given WHO diagnostic
numbers include HIV-associated lymphoma, germinal center B
cell-like subtype of diffuse large B cell lymphoma, activated B
cell-like subtype of diffuse large B-cell lymphoma, follicular
hyperplasia (non-malignant), and infectious mononucleosis
(non-malignant).
[0007] Although the WHO classification has proven useful in patient
management and treatment, patients assigned to the same WHO
diagnostic category often have noticeably different clinical
outcomes. In many cases, these different outcomes appear to be due
to molecular differences between tumors that cannot be readily
observed by analyzing tumor morphology. More precise methods are
needed for identifying and classifying lymphomas based on their
molecular characteristics.
SUMMARY
[0008] In certain embodiments, a composition is provided comprising
the set of probes listed in Table 2, which is contained in the file
entitled [0009] "Table_0002_LymphDx_Probe_List.txt." Preferably,
this composition comprises a microarray.
[0010] In certain embodiments, a method is provided for generating
a survival predictor for a particular lymphoma type. In this
method, one or more biopsy samples that have been diagnosed as
belonging to a particular lymphoma type are obtained. Gene
expression data is obtained for these samples, and genes with
expression patterns associated with longer or shorter survival are
identified. Hierarchical clustering is performed to group these
genes into gene expression signatures, and the expression of all
genes within each signature are averaged to obtain a gene
expression signature value for each signature. Those gene
expression signature values are then used to generate a
multivariate survival predictor.
[0011] In certain embodiments, a method is provided for predicting
survival in a follicular lymphoma (FL) subject. In this method, a
biopsy sample is obtained from the subject and gene expression data
is obtained from the biopsy sample. The expression level of those
genes belonging to an immune response-1 or immune response-2 gene
expression signature are averaged to generate gene expression
signature values for each signature. A survival predictor score is
then calculated using an equation:
[2.71*(immune response-2 gene expression signature
value)]-[2.36*(immune response-1 gene expression signature
value)].
A higher survival predictor score is associated with a less
favorable outcome. In one embodiment, the gene expression data used
in this method is obtained using a microarray.
[0012] In certain embodiments, another method is provided for
predicting survival in a follicular lymphoma (FL) subject. In the
method, a biopsy sample is obtained from the subject and gene
expression data is obtained from the biopsy sample. The expression
level of those genes belonging to a B cell differentiation, T-cell,
or macrophage gene expression signature are averaged to generate
gene expression signature values for each signature. A survival
predictor score is then calculated using an equation:
[2.053*(macrophage gene expression signature value)]-[2.344*(T-cell
gene expression signature value)]-[0.729*(B-cell gene expression
signature value)].
A higher survival predictor score is associated with a less
favorable outcome. In one embodiment, the gene expression data used
in this method is obtained using a microarray.
[0013] In certain embodiments, yet another method is provided for
predicting survival in a follicular lymphoma (FL) subject. In this
method, a biopsy sample is obtained from the subject and gene
expression data is obtained from the biopsy sample. The expression
level of those genes belonging to a macrophage, T-cell, or B-cell
differentiation gene expression signature are averaged to generate
gene expression signature values for each signature. A survival
predictor score is then calculated using an equation:
[1.51*(macrophage gene expression signature value)]-[2.11*(T-cell
gene expression signature value)]-[0.505*(B-cell differentiation
gene expression signature value)].
A higher survival predictor score is associated with a less
favorable outcome. In one embodiment, the gene expression data used
in this method is obtained using a microarray.
[0014] In certain embodiments, a method is provided for predicting
survival in a diffuse large B cell lymphoma (DLBCL) subject. In
this method, a biopsy sample is obtained from the subject and gene
expression data is obtained from the biopsy sample. The expression
level of those genes belonging to an ABC DLBCL high, lymph node, or
MHC class II gene expression signature are averaged to generate
gene expression signature values for each signature. A survival
predictor score is then calculated using an equation:
[0.586*(ABC DLBCL high gene expression signature
value)]-[0.468*(lymph node gene expression signature
value)]-[0.338*(MHC class II gene expression signature value)].
A higher survival predictor score is associated with a less
favorable outcome. In the embodiment, the pane expression data used
in this method is obtained using a microarray.
[0015] In certain embodiments, another method is provided for
predicting survival in a diffuse large B cell lymphoma (DLBCL)
subject. In this method, a biopsy sample is obtained from the
subject and gene expression data is obtained from the biopsy
sample. The expression level of those genes belonging to a lymph
node, germinal B cell, proliferation, or MHC class II gene
expression signature are averaged to generate gene expression
signature values for each signature. A survival predictor score is
then calculated using an equation:
[-0.4337*(lymph node gene expression
signature)]+[0.09*(proliferation gene expression
signature)]-[0.4144*(germinal center B-cell gene expression
signature)]-[0.2006*(MHC class II gene expression signature)].
A higher survival predictor score is associated with a less
favorable outcome. In one embodiment, the gene expression data used
in this method is obtained using a microarray.
[0016] In certain embodiments, yet another method is provided for
predicting survival in a diffuse large B cell lymphoma (DLBCL)
subject. In this method, a biopsy sample is obtained from the
subject and gene expression data is obtained from the biopsy
sample. The expression level of those genes belonging to a lymph
node, germinal B cell, or MHC class II gene expression signature
are averaged to generate gene expression signature values for each
signature. A survival predictor score is then calculated using an
equation:
[-0.32*(lymph node gene expression signature)]-[0.176*(germinal B
cell gene expression signature)]-[0.20*(MHC class II gene
expression signature)].
A higher survival predictor score is associated with a less
favorable outcome. In one embodiment, the gene expression data used
in this method is obtained using a microarray. In another
embodiment, the gene expression data is obtained using RT-PCR.
[0017] In certain embodiments, a method is provided for refining a
method for predicting survival in a diffuse large B cell lymphoma
(DLBCL). In this method, gains or amplifications of the 3p11-p12
region in chromosome 3 are identified, wherein gains or
amplifications of this region are associated with a less favorable
outcome. This information can be integrated into an existing method
for predicting DLBCL survival. For example, a survival predictor
score may be calculated using an equation such as:
Survival predictor score=[0.241*(proliferation gene expression
signature value)]+[0.310*(BMP6 expression value))-[0.290*(germinal
center B cell gene expression signature value)]-[0.311*(MHC class
II gene expression signature value)]-[0.249*(lymph node gene
expression signature value)].
wherein a higher survival predictor score is associated with a less
favorable outcome. The DLBCL sample may then be assayed for gains
or amplifications in the 3p11-p12 using any available method,
including for example CGH. The identification of gains or
amplifications in this region indicate a decrease in survival. This
information can be used to adjust the survival predictor score
accordingly. Alternatively, identification of a gain or
amplification of 3p11-p12 may be used as a stand-alone indicator of
less favorable outcome for a DLBCL patient in the absence of
additional gene expression data.
[0018] In certain embodiments, a method is provided for predicting
survival in a mantle cell lymphoma (MCL) subject. In this method, a
biopsy sample is obtained from the subject and gene expression data
is obtained from the biopsy sample. The expression level of those
genes belonging to a proliferation gene expression signature are
averaged to generate a gene expression signature value. A survival
predictor score is then calculated using an equation:
[1.66*(proliferation gene expression signature value)]. A higher
survival predictor score is associated with a less favorable
outcome. In one embodiment, the gene expression data used in this
method is obtained using a microarray.
[0019] In certain embodiments, a method is provided for determining
the probability that a sample X belongs to a first lymphoma type or
a second lymphoma type. In this method, a set of genes is
identified that is differentially expressed between the two
lymphoma types in question, and a set of scale factors representing
the difference in expression between the lymphoma types for each of
these genes are calculated. A series of linear predictor scores are
generated for samples belonging to either of the two lymphoma types
based on expression of these genes. Gene expression data is then
obtained for sample X, and a linear predictor score is calculated
for this sample. The probability that sample X belongs to the first
lymphoma type is calculated using an equation that incorporates the
linear predictor score of sample X and the mean and variance of the
linear predictor scores for the known samples of either lymphoma
type.
[0020] In certain embodiments, a method is provided for determining
the lymphoma type of a sample X. In this method, a set of genes is
identified that is differentially expressed between a first
lymphoma type and a second lymphoma type, and a set of scale
factors representing the difference in expression of each of these
genes between the two lymphoma types are calculated. A series of
linear predictor scores are generated for samples belonging to
either of the two lymphoma types based on expression of these
genes. Gene expression data is then obtained for sample X, and a
linear predictor score is calculated for this sample. The
probability that sample X belongs to the first lymphoma type is
calculated using an equation that incorporates the linear predictor
score of sample X and the mean and variance of the linear predictor
scores for the known samples of either lymphoma type. This entire
process is then repeated with various lymphoma types being
substituted for the first lymphoma type, the second lymphoma type,
or both.
[0021] In certain embodiments, a method is provided for determining
the lymphoma type of a sample X. In this method, a series of
lymphoma type pairs are created, with each pair consisting of a
first lymphoma type and a second lymphoma type. For each type pair,
gene expression data is obtained for a set of genes, and a series
of scale factors representing the difference in expression of each
of these genes between the two lymphoma types are calculated. A
subset of z genes with the largest scale factors are identified,
and a series of linear predictor scores are generated for samples
belonging to either of the two lymphoma types. Linear predictor
scores are calculated for anywhere from 1 to z of these genes. The
number of genes from 1 to z that results in the largest difference
in linear predictor scores between the two lymphoma types is
selected, and gene expression data for these genes is obtained for
sample X. A linear predictor score is generated for sample XT and
the probability that the sample belongs to the first lymphoma type
is calculated using an equation that incorporates the linear
predictor score for sample X and the mean and variance of the
linear predictor scores for the known samples of either lymphoma
type.
[0022] In certain embodiments, another method is provided for
determining the lymphoma type of a sample X. In this method, a
series of lymphoma type pairs are created, with each pair
consisting of a first lymphoma type and a second lymphoma type. For
each type pair, gene expression data is obtained for a set of
genes, and a series of scale factors representing the difference in
expression of each of these genes between the two lymphoma types
are calculated. The set of genes is divided into gene-list
categories indicating correlation with a gene expression signature.
Within each gene-list category, a subset of z genes with the
largest scale factors are identified, and a series of linear
predictor scores are generated for samples belonging to either of
the two lymphoma types. Linear predictor scores are calculated for
anywhere from 1 to z of these genes. The number of genes from 1 to
z that results in the largest difference in linear predictor scores
between the two lymphoma types is selected, and gene expression
data for these genes is obtained for sample X. A linear predictor
score is generated for sample X, and the probability q that the
sample belongs to the first lymphoma type is calculated using an
equation that incorporates the linear predictor score for sample X
and the mean and variance of the linear predictor scores for the
known samples of either lymphoma type. A high probability q
indicates that sample X belongs to the first lymphoma type, a low
probability q indicates that sample X belongs to the second
lymphoma type, and a "middle probability" indicates that sample X
belongs to neither lymphoma type. The cut-off point between high,
middle, and low probability values is determined by ranking samples
of known lymphoma type according to their probability values, then
analyzing every possible cut-off point between adjacent samples by:
3.99*[(% of first lymphoma type misidentified as second lymphoma
type)+(% of second lymphoma type misidentified as a flrst lymphoma
type)]+[(% of first lymphoma type identified as belonging to
neither lymphoma type)+(% of second lymphoma type identified as
belonging to neither lymphoma type)]. The final cut-off points are
those that minimize the value of this equation.
[0023] In certain embodiments, a method is provided for classifying
a sample as BL. In this method, a series of lymphoma type pairs are
created, with each pair consisting of a first lymphoma type (BL)
and a second lymphoma type. In certain embodiments, the second
lymphoma type is DLBCL, and in certain of these embodiments, the
DLBCL is ABC, GCB, or PMBL. For each type pair, gene expression
data is obtained for a set of genes, and a series of scale factors
representing the difference in expression of each of these genes
between the two lymphoma types are calculated. The set of genes is
divided into two subsets. The first subset includes c-myc and c-myc
target genes, while the second subset includes z genes from the
gene set that exhibit the largest scale factors and do not fall
into the first subset. In certain embodiments, z is 100. A first
and second series of linear predictor scores are generated for
samples belonging to either of the two lymphoma types, with the
first series based on expression of the first gene subset and the
second series based on expression of the second gene subset.
Expression of the first and second gene subsets is measured for
sample X, and a first and second linear predictor score is
generated for sample X based on the expression of the first and
second gene subsets, respectively. Two probabilities, q.sub.1 and
q.sub.2, are calculated using equations that incorporate the first
and second linear predictor scores for sample X, respectively, and
the mean and variance of the linear predictor scores for the known
samples of either lymphoma type. Sample X is classified as BL if
both q.sub.1 and q.sub.2 are greater than 90%.
[0024] In certain embodiments, a method is provided for identifying
a lymphoma sample as cyclin D1-negative MCL. In this method, a
candidate sample X is identified based on a lack of cyclin D1
expression. A series of lymphoma type pairs are created, with each
pair consisting of MCL and a second lymphoma type. For each type
pair, gene expression data is obtained for a set of genes G, and a
series of scale factors representing the difference in expression
of each of these genes between the two lymphoma types are
calculated. A subset of genes g with the largest scale factors are
identified, and a series of linear predictor scores are generated
for samples belonging to either of the two lymphoma types. Gene
expression data for the subset of genes g is obtained for sample X.
A linear predictor score is generated for sample X, and the
probability that the sample belongs to the first lymphoma type is
calculated using an equation that incorporates the linear predictor
score for sample X and the mean and variance of the linear
predictor scores for the known samples of either lymphoma type. A
probability greater than 90% indicates that the sample X is cyclin
D1-negative MCL.
BRIEF DESCRIPTION OF THE DRAWINGS
[0025] FIG. 1: Method for identifying lymphoma type. Flow chart
depicts a general method for identifying lymphoma type using gene
expression data.
[0026] FIG. 2: Survival signature analysis. Flow chart depicts
method for developing a lymphoma survival predictor based on gene
expression patterns.
[0027] FIG. 3: FL survival data. Survival data for 191 subjects
diagnosed with FL. Median age at diagnosis was 51 years (ranging
from 23 to 81 years), and the subjects had a median follow-up of
6.6 years (8.1 years for survivors, with a range of <1 to 26.2
years).
[0028] FIG. 4: Hierarchical clustering of survival associated genes
in FL samples. Each column represents a single FL sample, while
each row represents a single gene. Relative gene expression is
depicted according to the color scale at the bottom of the figure.
The dendrogram to the left indicates the degree to which the
expression pattern of each gene is correlated with that of the
other genes. The colored bars indicate sets of coordinated
regulated genes defined as gene expression signatures. Genes
comprising the immune response-1 and immune response-2 gene
expression signature are listed on the right.
[0029] FIG. 5: Kaplan-Meier plot of survival in FL samples based on
survival predictor scores. 191 FL samples were divided into
quartiles based on their survival predictor scores. The survival
predictor scores were calculated by:
[(2.71*immune*response-2 gene expression signature
value)]-[(2.36.times.immune response-1 gene expression signature
value)].
[0030] FIG. 6: Kaplan-Meier plot of aurvlvalln FL samples based on
IPI score. 96 FL samples were divided into three groups based on
their IPI scores.
[0031] FIG. 7: Kaplan-Meier plot of survival in FL samples with low
or high risk IPI scores based on survival predictor scares. 96 FL
samples with low risk (left panel) or intermediate risk (right
panel) IPI scores were divided into quartiles based on their
survival predictor scores. The survival predictor scores were
calculated by:
[(2.71*immune response-2 gene expression signature
value)]-[(2.36.times.immune response-1 gene expression signature
value)].
[0032] FIG. 8: Kaplan-Meier plot of survival in FL samples based on
survival predictor scores. 191 FL samples were divided into
quartiles based on their survival predictor scores. The survival
predictor scores were calculated by:
[2.053*(macrophage gene expression signature value)]-[2.344*(T-cell
gene expression signature value)]-[0.729*(B-cell differentiation
gene expression signature value)].
[0033] FIG. 9: Kaplan-Meier plot of survival in FL samples based on
survival predictor scores. 191 FL samples were divided into
quartiles based on their survival predictor scores. The survival
predictor scores were calculated by:
[1.51*(macrophage gene expression signature value)]-[2.11*(T-cell
gene expression signature value)-[0.505*(B-cell differentiation
gene expression signature value)].
[0034] FIG. 10: Kaplan-Meier plot of survival in DLBCL samples
based oh survival predictor scores. 231 DLBCL samples were divided
into quartiles based on their survival predictor scores. The
survival predictor scores were calculated by:
[0.586*(ABC DLBCL high gene expression signature
value)]-[0.468*[lymph node gene expression signature
value)]-[(0.336*MHC Class II gene expression signature value)].
[0035] FIG. 11: Kaplan-Meier plot of survival in DLBCL samples
based on survival predictor scores. 200 DLBCL samples were divided
into quartiles based on their survival predictor scores. The
survival predictor scores were calculated by:
[-0.4337*(lymph node gene expression signature
value)]+[0.09*(proliferation gene expression,signature
value)]-[0.4144*(germinal center B-cell gene expression signature
value)]-[0.2006*(MHC class II gene expression signature
value)].
[0036] FIG. 12: Kaplan-Meier plot of survival in DLBCL samples
based on survival predictor scores. 200 DLBCL samples were divided
into quartiles based on their survival predictor scores. The
survival predictor scores were calculated by:
[-0.32*(lymph node gene expression signature
value)]-[0.176*(germinal center B-cell gene expression signature
value)]-[0.206*(MHC class II gene expression signature value)].
[0037] FIG. 13: Kaplan-Meier plot of survival in MCL samples based
on survival predictor scores. 21 MCL samples were divided into two
equivalent groups based on their survival predictor scores. The
survival predictor scores were calculated by:
1.66*(proliferation gene expression signature value).
[0038] FIG. 14: Kaplan-Meier plot of survival in MCL samples based
on survival predictor scores. 21 MCL samples were divided into two
equivalent groups based on their survival predictor scores. The
survival predictor scores were calculated by:
1.66*(proliferation gene expression signature value).
[0039] FIG. 15: Predicting lymphoma type using Bayesian analysis.
Bayes' rule can be used to determine the probability that an
unknown sample belongs to a first lymphoma type rather than a
second lymphoma type. A linear predictor score is generated for the
sample, and the probability that the sample belongs to the first
lymphoma type is determined based on the distribution of linear
predictor scores within the first and second lymphoma type.
[0040] FIG. 16: Performance of MCL predictor model. Results of the
gene-expression based predictor model for MCL are shown for three
models (MCL vs. ABC, MCL vs. GCB, MCL vs. SLL). Performance is
shown for both the training set and the validation set.
[0041] FIG. 17: Gene expression-based identification of DLBCL.
Expression levels for 27 genes in a subgroup predictor are shown
for 274 DLBCL samples. Expression levels are depicted according to
the color scale shown at the left. The 14 genes used to predict the
DLBCL subgroups in the Affymetrix data set are indicated with
asterisks. The probabilities that the DLBCL samples belong to the
ABC or GCB subtypes are graphed at the top, and the DLBCL cases are
arranged accordingly. Cases belonging to either ABC or GCB with 90%
or greater probability are indicated.
[0042] FIG. 18: Performance of DLBCL subtype predictor model.
Assignments of DLBCL samples to the ABC or GCB subtypes based on
hierarchical clustering vs. the predictor model disclosed herein
are compared within the training, validation, and total set of
samples.
[0043] FIGS. 19A and 19B: Relationship of gene expression in normal
B cell subpopulations to DLBCL subtypes. Relative gene expression
in the indicated purified B cell populations is depicted according
to the color scale in FIG. 17. The P value of the difference in
expression of these genes between the GCB and ABC DLBCL subtypes is
shown, and the subtype with the higher expression is shown is
indicated (blue, ABC; orange, GCB). FIG. 19A. DLBCL subtype
distinction genes that are more highly expressed in germinal center
B cells than at other B cell differentiation stages. FIG. 19B.
DLBCL subtype distinction genes that are more highly expressed in
plasma cells than at other B cell differentiation stages.
[0044] FIGS. 20A and 20B: Identification of a PMBL gene expression
signature. FIG. 20A. Hierarchical clustering identified a set of 23
PMBL signature genes that were more highly expressed in most
lymphomas with a clinical diagnosis of PMBL than in lymphomas
assigned to the GCB or ABC subtypes. Each row presents gene
expression measurements from a single Lymphochip microarray feature
representing the genes indicated. Each column represents a single
lymphoma biopsy sample. Relative gene expression is depicted
according to the color scale shown. FIG. 20B. Hierarchical
clustering of the lymphoma biopsy samples based on expression of
the PMBL signature genes identified in (A). A "core" cluster of
lymphoma cases was identified that highly expressed the PMBL
signature genes.
[0045] FIGS. 21A and 21B: Development of a gene expression-based
molecular diagnosis of PMBL. FIG. 21A. A PMBL predictor was created
based on expression of the 46 genes shown. Relative gene expression
for each lymphoma biopsy sample is presented according to the color
scale shown in FIG. 20. The probability that each sample is PMBL or
DLBCL based on gene expression is shown at the top. FIG. 21B. The
PMBL predictor was used to classify 274 lymphoma samples as PMBL or
DLBCL. Prediction results are summarized on the right, and the
relative gene expression for each case that was classified by the
predictor as PMBL is shown on the left. Average expression of each
gene in samples classified as DLBCL is also shown. The 20 genes
listed are those represented on the Lymphochip that were more
highly expressed in PMBL than in DLBCL. Not shown are eight genes
from the PMBL predictor that were more highly expressed in DLBCL
than in PMBL.
[0046] FIG. 22: Clinical characteristics of PMBL patients.
Kaplan-Meier plot of overall survival in PMBL, GCB, and ABC
patients after chemotherapy.
[0047] FIG. 23: Optimization of gene number in lymphoma predictor.
The optimal number of genes for inclusion in the lymphoma type
predictor model is that number which generates a maximum
t-statistic when comparing the LPS of two samples from different
lymphoma types.
[0048] FIG. 24: LPS distribution among FL and DLBCL/BL samples.
Standard and proliferation LPSs for FL (.times.) and DLBCL/BL (+)
samples. Dotted lines indicate standard deviations from the fitted
multivariate normal distributions.
[0049] FIG. 25: Determination of cut-off points for lymphoma
classification. The cut-off points between samples classified as
DLBCL/BL, FL, or unclassified were optimized to minimize the number
of samples classified as the wrong lymphoma type. The optimal lower
cut-off point was at q=0.49, while the optimal upper cut-off point
was at q=0.84.
[0050] FIG. 26: Division of LPSs among FL and DLBCL/FL samples.
Illustrations of how the cut-off points described in FIG. 25
divided the space between the LPSs of FL (.times.) and DLBCL/BL (+)
samples.
[0051] FIG. 27: Lymphoma classification results. Results of
lymphoma classification based on gene expression. 100% of SLL, MCL,
and FH samples were classified correctly, and only 3% of DLBCL/BL
and FL samples were classified incorrectly.
[0052] FIG. 28: DLBCL subtype classification based on gene
expression. None of the ABC samples were classified as the wrong
subtype, while only one of the BL samples was classified
incorrectly. Of the GCB and PMBL samples, only 5% and 6%,
respectively, were classified incorrectly.
[0053] FIGS. 29A-29D: Summary of chromosomal imbalances in DLBCL
samples. Chromosomal alterations in 224 untreated DLBCL samples
were classified by gene expression profiling. Each bar represents a
chromosomal region gained or lost in a single sample. Red bars on
left side of ideogram represent losses of chromosomal material.
Green bars on the right side of the ideogram represent gains of
chromosomal material. Thick green bars represent chromosomal gains
exceeding the cut-off value of 1.5 in a large chromosomal region,
and solid dots represent high-level DNA amplifications. FIG. 29A.
Chromosomal alterations in GCB samples (n=87).
[0054] FIG. 29B. Chromosomal alterations in ABC samples (n=77).
FIG. 29C. Chromosomal alterations in PMBL samples (n=19). FIG. 29D.
Diagram indicating frequencies of chromosomal imbalances that
distinguish between ABC, GCB, and PMBL. All differences were
statistically significant at p<0.05, with the exception of 12q12
gains (P=0.059).
[0055] FIGS. 30A-30F: Influence of chromosomal gains and
amplifications on locus-specific gene expression levels. Changes in
gene expression levels are depicted for each gene (averaged in each
cohort) with regard to locus-specific genetic status (wild-type vs.
gain vs. amplification). Genes are ordered according to their
chromosomal position. Gene locus information was obtained from the
web site for Genes On Sequence Map (Homo sapiens built 33). For
genes represented by more than one element on the Lymphochip, the
average expression of different clones was calculated. The black
bar on the left indicates the minimally gained region in all cases.
Expression level comparisons were performed using the ANOVA test.
Genes with significant differences (P<0.01) are highlighted in
red.
[0056] FIG. 31: Effect of chromosomal imbalances on gene expression
signatures, in each of the 4 panels, DLBCL cases are ordered
according to their average expression of the following gene
expression signatures: lymph node, proliferation, T cell, and MHC
class II. Samples with the chromosomal abnormalities shown on the
right are marked with a yellow bar. Correlations with a
P-value<0.05 are shown. If more than one cytoband in one
chromosomal arm showed a P-value<0.05, the cytoband with the
lowest p-value is displayed.
[0057] FIG. 32: Impact of genomic gains of 3p11-p12 on survival of
DLBCL patients. Kaplan-Meier survival estimates of DLBCL patients
with genomic gains of 3p11-p12 in comparison to their
stratification into survival quartiles based on the gene expression
based outcome predictor model alone 3 (Q=Quartile) (P=0.029).
[0058] FIG. 32: Kaplan-Meier plot of survival on DLBCL samples
based on survival predictor scores. The survival predictor was
calculated by:
[0.241*(proliferation gene expression signature
value)]+[0.310*(BMP69 -[0.290*(germinal center B cell gene
expression signature value)]-[0.311*(MHC class II gene expression
signature value)]-0.249*(lymph node gene expression signature
value)],
with chromosome 3 gains involving the 3p11-p12 region considered as
an independent prognostic indicator.
[0059] FIG. 33: Gene expression profiles of MCL signature genes in
cyclin D1-negative MCL cases. Expression profiles for cyclin
D1-negative MCL cases were compared to those of ABC, GCB, PMBL, FL,
MALT, SMZL, SLL, and MCL. Median expression levels of the MCL
signature genes are shown. For the cyclin-D1 MCL cases, each column
represents a single lymphoma specimen and each row represents the
level of expression of a single gene in the MCL signature. Red
squares indicate increased expression. Green squares indicate
decreased expression relative to the median expression level
according to the color scale shown over a four-fold range. The
lower panel shows expression levels of the D-type cyclins according
to the color scale over a sixteen-fold range.
[0060] FIGS. 34A-34D: Cytologic features and expression of D-type
cyclins in cyclin D1-negative MCL. FIG. 34A. Typical MCL cytology
(case 1) (hematoxylin and eosin stain, original magnification
.times.500). FIG. 34B. Cyclin D1 protein, showing only a rare
non-tumor cell with nuclear staining (case 1). FIG. 34C. Cyclin D2
protein, showing strong nuclear staining of the tumor cells (case
2). FIG. 34D. Cyclin D3 protein, showing strong nuclear staining of
the tumor cells (case 4) (immunoperoxidase stains, original
magnification .times.400).
[0061] FIGS. 35A-35D: Molecular predictor of BL. FIG. 35A.
Distinction between BL and DLBCL using gene expression. Each row
represents the expression level of a gene and each column
represents a lymphoma sample. Relative gene expression levels are
depicted according to the color scale shown. Stage one utilized
c-myc and its target genes. Stage two utilized 100 additional genes
that distinguish BL from ABC, GCB, or PMBL. The panel includes only
those cases for which the pathology-based diagnosis and the gene
expression-based diagnosis agreed. FIG. 35B. Creation of an
unbiased list of c-myc target genes using RNA-interference
experiments. The OCl-Ly10 DLBCL cell line was transfected by
electroporation with small interfering RNAs targeting the c-myc
gene, and gene expression was compared to that of
control-transfected cells by DNA microarray at the indicated times
post-transfection. Downregulation of c-myc and its targets is
depicted in green according to the color scale shown. FIG. 35C.
Performance of the gene expression-based predictor according to
leave-one-out cross-validation analysis. Samples submitted as BL or
Burkitt-like lymphoma were classified upon pathology review as
classic and atypical BL. Samples submitted as DLBCL were further
classified by gene expression as ABC, GCB, PMBL, or unclassified.
FIG. 35D. Classification of samples submitted as BL or Burkitt-like
lymphoma that were reclassified as either DLBCL or high grade
lymphoma not otherwise specified. Also shown are samples submitted
and verified as high grade DLBCL. Those cases for which the
pathology-based diagnosis and the gene expression-based diagnosis
disagreed (BL-discrepant cases) are marked with an asterisk.
[0062] FIGS. 36A and 36B: Performance of a molecular predictor of
BL. FIG. 36A. Gene expression in the nine BL-discrepant cases for
which the pathology-based diagnosis and the gene expression-based
diagnosis were not in agreement. Expression of the BL-predictor
genes in these samples is compared to the average expression of
these genes in BL and DLBCL. For each sample, immunophenotype, BCL2
mRNA and protein expression, and t(14;18) FISH results are depicted
at the bottom of the panel. Also shown is the probability that each
sample is BL based on gene expression. FIG. 36B. Expression of the
BL-predictor genes in the six DLBCL samples known to harbor a
translocation involving the c-myc gene. Expression of these genes
in the samples is compared to the average expression in BL and
DLBCL The probability that each sample is BL based on gene
expression is shown.
[0063] FIGS. 37A-37E: Relative expression of gene expression
signatures among lymphoma subtypes. FIG. 37A. Average relative
expression of c-myc end its target genes for BL and each molecular
subtype of DLBCL (ABC, GCB, and PMBL). All expression data are
shown over a 4-fold range. The color scale is identical to that in
FIG. 36. FIG. 37B. Expression of genes related to normal GCB cell
differentiation among the lymphoma subtypes. "BL-high" genes are
expressed at 2-fold or higher levels in BL compared to GCB
(P<0.001). "BL-low" genes are expressed at 2-fold or higher
levels in GCB compared to BL (P<0.001). The "BL-GCB" genes are
not differentially expressed between BL and GCB. FIG. 37C. Relative
expression among lymphoma types of genes that encode MHC class-1
proteins. FIG. 37D. Relative expression among the lymphoma types of
genes that are targets of the NF-.kappa.B signaling pathway. FIG.
37E. Average expression of each of the four gene expression
signatures among the lymphoma samples according to their
classification by the BL-predictor.
[0064] FIGS. 38A-38D: Survival analysis in BL and DLBCL FIG. 38A.
Kaplan-Meier plot of overall survival for all patients with a gene
expression-based diagnosis of BL, subdivided by treatment received.
FIG. 38B. Kaplan-Meier plot of overall survival for adults with a
gene expression-based diagnosis of BL, subdivided by treatment
received. FIG. 38C. Kaplan-Meier plot of overall survival for all
BL-discrepant patients, subdivided by treatment received. FIG. 38D.
Kaplan-Meier plot of overall survival for all patients assigned to
the three molecular subgroups of DLBCL.
DETAILED DESCRIPTION
[0065] The following description is merely intended to illustrate
various embodiments of the invention. As such, the specific
modifications discussed are not to be construed limitations on the
scope of the invention. It will be apparent to one skilled in the
art that various equivalents, changes, and modifications may be
made without departing from the scope of the invention, and it us
understood that such embodiments are to be included herein.
Abbreviations
[0066] The following abbreviations are used herein: ABC, activated
B-cell-like diffuse large B cell lymphoma; ASCT, autologous stem
cell transplant; AWD, alive with disease; BL, Burkitt lymphoma; BM,
bone marrow; CGH, comparative genome hybridization; CHOP,
cyclophosphamide, doxorubtcine, vincristine, and prednisone; CI,
confidence interval; CNS, central nervous system; COP,
cyclophosphamide, vincristine; and prednisone; C.sub.T, cycle
threshold; DLBCL, diffuse large B-cell lymphoma; DOD, dead of
disease; ECOG, Eastern Cooperative Oncology Group; EST, expressed
sequence tag; FACS, fluorescence-activated cell sorting; FH,
follicular hyperplasia; FISH, fluorescence in-situ hybridization;
FL, follicular lymphoma; GC, germinal center, GGB, germinal center
B-cell-like diffuse large B cell lymphoma; GI gastrointestinal;
IPI, International Prognostic Index; LPC, lymphoplasmacytic
lymphoma; LPS, linear predictor score; MALT, mucosa-associated
lymphoid tissue lymphomas; MCL, mantle cell lymphoma; MHC, major
histocompatibility complex; NA, not available or not applicable;
NK, natural killer; NMZ, nodal marginal zone lymphoma; PB,
peripheral blood; PCR, polymerase chain reaction; PMBL, primary
mediastinal B-cell lymphoma; PR, partial response; PTLD,
post-transplant lympho proliferative disorder; REAL, Revised
European-American Lymphoma; RPA, RNase protection assay; RQ-PCR,
real-time quantitative PCR; RR, relative risk of death; RT-PCR,
reverse transcriptase polymerase chain reaction; SAGE, serial
analysis of gene expression; SLL, small lymphocytic lymphoma; SMZL,
splenic marginal zone lymphoma; WHO, World Health Organization.
Definitions
[0067] The term "lymphoproliferative disorder" as used herein
refers to any tumor of lymphocytes, and may refer to both malignant
and benign tumors. The terms "lymphoma" and "lymphoid malignancy"
as used herein refer specifically to malignant tumors derived from
lymphocytes and lymphoblasts. Examples of lymphomas include, but
are not limited to, follicular lymphoma (FL), Burkitt lymphoma
(BL), mantle cell lymphoma (MCL), follicular hyperplasia (FH),
smallcell lymphocytic lymphoma (SLL), mucosa-associated lymphoid
tissue lymphoma (MALT), splenic lymphoma, multiple myeloma,
lymphoplasmacytic lymphoma, post-transplant lymphoproliferative
disorder (PTLD), lymphoblastic lymphoma, nodal marginal zone
lymphoma (NMZ), germinal canter B cell-like diffuse large B cell
lymphoma (GGB), activated B cell-like diffuse large B cell lymphoma
(ABC) and primary mediastinal B cell lymphoma (PMBL).
[0068] The phrase "lymphoma type" (or simply "type") as used herein
refers to a diagnostic classification of a lymphoma. The phrase may
refer to a broad lymphoma class (e.g., DLBCL, FL, MCL, etc.) or to
a subtype or subgroup falling within a broad lymphoma class (e.g.,
GCB DLBCL, ABC DLBCL).
[0069] The phrase "gene expression data" as used herein refers to
information regarding the relative or absolute level of expression
of a gene or set of genes in a cell or group of cells. The level of
expression of a gene may be determined based on the Jevel of
RNA,-such as mRNA, encoded by the gene. Alternatively, the level of
expression may be determined based on the level of a polypeptide or
fragment thereof encoded by the gene, "Gene expression data" may be
acquired for an individual cell, or for a group of cells such as a
tumor or biopsy sample.
[0070] The term "microarray," "array," or "chip" refers to a
plurality of nucleic acid probes coupled to the surface of a
substrate in different known locations. The substrate is preferably
solid. Microarrays have been generally described in the art in, for
example, U.S. Pat. No. 5,143,854 (Plrrung), U.S. Pat. No. 5,424,188
(Fodor), U.S. Pat. No. 5,445,934 (Fodor), U.S. Pat. No. 5,677,195
(Winkler), U.S. Pat. No. 5,744,305 (Fodor), U.S. Pat. No. 5,800,992
(Fodor), U.S. Pat. No. 6,040,193 (Winkler), and Fodor et at. 1991.
Light-directed, spatially addressable parallel chemical synthesis.
Science, 251; 767-777. Each of these references is incorporated by
reference herein in their entirety.
[0071] The term "gene expression signature" or "signature" as used
herein refers to a group of coordinately expressed genes. The genes
making up this signature may be expressed in a specific cell
lineage, stage of differentiation, or during a particular
biological response. The genes can reflect biological aspects of
the tumors in which they are expressed, such as the cell of origin
of the cancer, the nature of the non-malignant cells in the biopsy,
and the oncogenic mechanisms responsible for the cancer (Shaffer
2001). Examples of gene expression signatures include lymph node
(Shaffer 2001), proliferation (Rosenwald 2002), MHC class II, ABC
DLBCL high, B-cell differentiation, T-cell, macrophage, immune
response-1, immune response-2, and germinal center B cell.
[0072] The phrase "survival predictor score" as used herein refers
to a score generated by a multivariate model used to predict
survival based on gene expression-A subject with a higher survival
predictor score is predicted to have poorer survival than a subject
with a lower survival predictor score.
[0073] The term "survival" as used herein may refer to the
probability or likelihood of a subject surviving for a particular
period of time. Alternatively, it may refer to the likely term of
survival for a subject, such as expected mean or median survival
time for a subject with a particular gene expression pattern,
[0074] The phrase "linear predictor score" or "LPS" as used herein
refers to a score that denotes the probability that a sample
belongs to a particular lymphoma type. An LPS may be calculated
using an equation such as:
LPS ( S ) = j = 0 t j S j , ##EQU00001##
where S.sub.j is the expression of gene j from gene set G in a
sample S, and t.sub.j is a scale factor representing the difference
in expression of gene j between a first lymphoma type and a second
lymphoma type. Alternatively, a linear predictor score may be
generated by other methods including but not limited to linear
discriminant analysis (Dudolt 2002), support vector machines (Furey
2000), or shrunken centroids (Tibshiranl 2002)
[0075] The phrase "scale factor" as used herein refers to a factor
that defines the relative difference in expression of a particular
gene between two samples. An example of a scale factor is a t-score
generated by a Student's t-test.
[0076] The phrase "lymphoma subject," wherein "lymphoma" is a
specific lymphoma type (e.g., "follicular lymphoma subject"), may
refer to a subject that has been diagnosed with a particular
lymphoma by any method known in the art or discussed herein. This
phrase may also refer to a subject with a known or suspected
predisposition or risk of developing a particular lymphoma
type.
[0077] The gene expression profile of a cancer cell or biopsy
sample at a specific timepoint may provide the basis for better
classification of cancer subtypes, more accurate prediction of
cancer survival, and more specifically, tailored-therapies.
Disclosed herein are a variety of methods for identifying,
diagnosing, and/or classifying a lymphoma, lymphoid malignancy, or
lymphoproliferative disorder based on its gene expression patterns.
Also disclosed are methods for predicting survival in a subject
diagnosed with a particular lymphoma type or subtype using gene
expression data. The information obtained using these methods will
be useful in evaluating the optimal therapeutic approach to be
employed for a particular subject suffering from cancer.
[0078] The pattern of expression of a particular gene is closely
connected to the biological role and effect of its gene product.
For this reason, the systematic study of variations in gene
expression provides an alternative approach for linking specific
genes with specific diseases and for recognizing heritable gene
variations that are important for immune function. For example,
allelic differences in the regulatory region of a gene may
influence the expression levels of that gene. An appreciation for
such quantitative traits in the immune system may help elucidate
the genetics of autoimmune diseases and lymphoprollferative
disorders.
[0079] Genes that encode components of the same multi-subunit
protein complex are often coordinately regulated. Coordinate
regulation is also observed among genes whose products function in
a common differentiation program or in the same physiological
response, pathway. Recent application of gene expression profiling
to the immune system has shown that lymphocyte differentiation and
activation are accompanied by parallel changes in expression among
hundreds of genes. Gene expression databases may be used to
interpret the pathological changes in gene expression that
accompany autoimmunity, immune deficiencies, cancers of immune
cells and of normal immune responses.
[0080] Scanning and interpreting large bodies of relative gene
expression data is a formidable task. This task is greatly
facilitated by algorithms designed to organize the data in a way
that highlights systematic features, and by visualization tools
that represent the differential expression of each gene as varying
intensities and hues of color (Elsen 1998). The development of
microarrays, which are capable of generating massive amounts of
expression data in a single experiment, has greatly increased the
need for faster and more efficient methods of analyzing large-scale
expression data sets. In order to effectively utilize microarray
gene expression data for the identification and diagnosis of
lymphoma and for the prediction of survival in lymphoma patients,
new algorithms must be developed to identify important information
and convert it to a mare manageable format. In addition, the
microarrays used to generate this data should be streamlined to
incorporate probe sets that are useful for diagnosis and survival
prediction. Disclosed herein are various methods and compositions
that address both of these issues.
[0081] Mathematical analysis of gene expression data is a rapidly
evolving science based on a rich mathematics of pattern recognition
developed in other contexts (Kohonen 1997). Mathematical analysis
of gene expression generally has three goals. First, it may be used
to identify groups of genes that are coordinately regulated within
a biological system. Second, it may be used to recognize and
interpret similarities between biological samples on the basis of
similarities in gene expression patterns. Third, it may be used to
recognize and identify those features of a gene expression pattern
that are related to distinct biological processes or
phenotypes.
[0082] Mathematical analysis of gene expression data often begins
by establishing the expression pattern for each gene on an array
across n experimental samples. The expression pattern of each gene
can be represented by a point in n-dimensional space, with each
coordinate specified by an expression measurement in one of the n
samples (Elsen 1998). A clustering algorithm that uses distance
metrics can then be applied to locale clusters of genes in this
n-dimensional space. These clusters indicate genes with similar
patterns of variation in expression over a series of experiments.
Clustering methods that have been applied to microarray data in the
past include hierarchical clustering (Elsen 1998), self-organizing
maps (SOMs) (Tamayo 1999), k-means (Tavazole 1999), and
deterministic annealing (Alon 1999). A variety of different
algorithms, each emphasizing distinct orderly features of the data,
may be required to glean the maximal biological insight from a set
of samples (Alizadeh 1998). One such algorithm, hierarchical
clustering, begins by determining the gene expression correlation
coefficients for each pair of the n genes studied. Genes with
similar gene expression correlation coefficients are grouped next
to one another in a hierarchical fashion.
[0083] Generally, genes with similar expression patterns under a
particular set of conditions encode protein products that play
related roles in the physiological adaptation to those conditions.
Novel genes of unknown function that are clustered with a large
group of functionally related genes are likely to participate in
the same biological process. Likewise, the other clustering methods
mentioned herein may also group genes together that encode proteins
with related biological function.
[0084] Gene expression maps may be constructed by organizing gene
expression data from multiple samples using any of the various
clustering algorithms outlined herein. The ordered tables of data
may then be displayed graphically in a way that allows researchers
and clinicians to assimilate both the choreography of gene
expression on a broad scale and the fine distinctions in expression
of individual genes.
[0085] In such a gene expression map, genes that ate clustered
together reflect a particular biological function, and are termed
gene expression signatures (Shaffer 2001). One general type of gene
expression signature includes genes that are characteristically
expressed in a particular cell type or at a particular stage of
cellular differentiation or activation. Another general type of
gene expression signature includes genes that are regulated in
their expression by a particular biological process such as
proliferation, or by the activity of a particular transcription
factor or signaling pathway.
[0086] The pattern of gene expression in a biological sample
provides a distinctive and accessible molecular picture of its
functional state and identity (DeRisi 1997; Cho 1998; Chu 1998;
Holstege 1998; Spellman 1998). Each cell transduces variations in
its environment, internal state, and developmental state into
readily measured and recognizable variations in its gene expression
patterns. Two different samples that have related gene expression
patterns are therefore likely to be biologically and functionally
similar to one another. Some biological processes are reflected by
the expression of genes in a specific gene expression signature, as
described above. The expression of a specific gene expression
signature in a sample can provide important biological insights
into its cellular composition and the function of various
intracellular pathways within those cells.
[0087] The present invention discloses a variety of gene expression
signatures related to the clinical outcome of lymphoma patients.
While several of these signatures share a name with a previously
disclosed signature, each of the gene expression signatures
disclosed herein comprises a novel combination of genes. For
example, the lymph node signature disclosed herein includes genes
encoding extracellular matrix components and genes that are
characteristically expressed in macrophage, NK, and T cells (e.g.,
.alpha.-Actinin, collagen type III .alpha. 1, connective tissue
growth factor, fibronectin, KIAA0233, urokinase plasminogen
activator). The proliferation signature includes genes that are
characteristically expressed by cells that are rapidly multiplying
or proliferating (e.g., c-myc, E21G3, NPM3, BMP6). The MHC class II
signature includes genes that interact with lymphocytes in order to
allow the recognition of foreign antigens (e.g., HLA-DP.alpha.,
HLA-DQ.alpha., HLA-DR.alpha., HLA-DR.beta.). The immune response-1
signature includes genes encoding T cell markers (e.g., CD7, CD8B1,
ITK, LEF1, STAT4), as well as genes that are highly expressed in
macrophages (e.g., ACTN1, TNFSF13B). The immune response-2
signature includes genes known to be preferentially expressed in
macrophages and/or dendritic cells (e.g., TLR6, FCGR1A, SEPT10,
LGMN, C3AR1). The germinal center B cell signature includes genes
known to be overexpressed at this stage of B cell differentiation
(e.g., MME, MEF2C, BCL6, LMO2, PRSPAP2, MBD4, EBF,MYBL1).
[0088] Databases of gene expression signatures have proven quite
useful in elucidating the complex gene expression patterns of
various cancers. For example, expression of genes from the germinal
center B-cell signature in a lymphoma biopsy suggests that the
lymphoma is derived from this stage of B cell differentiation. In
the same lymphoma biopsy, the expression of genes from the T cell
signature can be used to estimate the degree of infiltration of the
tumor by host T cells, while the expression of genes from the
proliferation signature can be used to quantitate the tumor cell
proliferation rate. In this manner, gene expression signatures
provide an "executive summary" of the biological properties of a
tumor specimen. Gene expression signatures can also be helpful in
interpreting the results of a supervised analysis of gene
expression data. Supervised analysis generates a long list of genes
with expression patterns that are correlated with survival. Gene
expression signatures can be useful in assigning these "predictive"
genes to functional categories. In building a multivariate model of
survival based on gene expression data, this functional
categorization helps to limit the inclusion of multiple genes in
the model that measure the same aspect of tumor biology.
[0089] Gene expression profiles can be used to create multivariate
models for predicting survival. The methods for creating these
models are called "supervised" because they use clinical data to
guide the selection of genes to be used in the prognostic
classification. For example, a supervised method might identify
genes with expression patterns that correlate with the length of
overall survival following chemotherapy. The general method used to
create a multivariate model for predicting survival may utilize the
following steps: [0090] 1. Identify genes with expression patterns
that are univariately associated with a particular clinical outcome
using a Cox proportional hazards model. Generally, a univariate
p-value of <0.01 is considered the cut-off for significance.
These genes are termed "predictor" genes. [0091] 2. Within a set of
predictor genes, identify gene expression signatures. [0092] 3. For
each gene expression signature that is significantly-associated
with survival, average the expression of the component genes within
this signature to generate a gene expression signature value.
[0093] 4. Build a multivariate Cox model of clinical outcome using
the gene expression signature values. [0094] 5. If possible,
include additional genes in the model that do not belong to a gene
expression signature but which add to the statistical power of the
model. This approach has been utilized in the present invention to
create novel survival prediction models for FL, DLBCL, and MCL.
Each of these models generates a survival predictor score, with a
higher score being associated with worse clinical outcome. Each of
these models may be used separately to predict survival.
Alternatively, these models may be used in conjunction with one or
more other models, disclosed herein or in other references, to
predict survival.
[0095] A first FL survival predictor was generated using gene
expression data obtained using Affymetrix U133A and U133B
microarrays. This predictor incorporated immune response-1 and
immune response-2 gene expression signatures. Fitting the Cox
proportional hazards model to the gene expression signature values
obtained from these signatures resulted in the following model:
Survival predictor score=[(2.71*immune response-2 gene expression
signature value)]-[(2.36.times.immune response-1 gene expression
signature value)].
[0096] A second FL survival predictor was generated using gene
expression data obtained using Affymetrix U133A and U133B
microarrays. This predictor incorporated macrophage, T-cell, and
B-cell differentiation gene expression signatures. Fitting the Cox
proportional hazards model to the gene expression signature values
obtained from these signatures resulted in the following model;
Survival predictor score=[2.053*(macrophage gene expression
signature value)]-[2.344*(T-cell gene expression signature
value)]-[0.729*(B-cell differentiation gene expression signature
value)].
[0097] A third FL survival predictor was generated using gene
expression data obtained using the Lymph Dx microarray. This
predictor incorporated macrophage, T-cell, and B-cell
differentiation gene expression signatures. Fitting the Cox
proportional hazards model to the gene expression signature values
obtained from these signatures resulted in the following model:
Survival predictor score=[1.51*(macrophage gene expression
signature value)]-[2.11*(T-cell gene expression signature
value)]-[0.505*(B-cell differentiation gene expression signature
value)].
[0098] A first DLBCL survival predictor was generated using gene
expression data obtained using Affymetrix U133A and U133B
microarrays. This predictor incorporated ABC DLBCL high, lymph
node, end MHC class II gene expression signatures. Fitting the Cox
proportional hazards model to the gene expression signature values
obtained from these signatures resulted in the following model:
Survival predictor score=[0.586*(ABC DLBCL high gene expression
signature value)]-[0.468*(fymph node gene expression signature
value)]-0.336*(MHC class II gene expression signature value)].
[0099] A second DLBCL survival predictor was generated using gene
expression data obtained using the Lymph Dx microarray. This
predictor incorporated lymph node, proliferation, germinal center
B-cell, and MHC class II gene expression signatures. Fitting the
Cox proportional hazards model to the gene expression signature
values obtained from these signatures resulted in the following
model:
Survival predictor score=[-0.4337*(lymph node gene expression
signature value)]+[0.09*(proliferation gene expression signature
value)]-0.4144*(germinal center B-cell gene expression signature
value)]-(0.2006*(MHC class II gene expression signature
value)].
[0100] A third DLBCL survival predictor was generated using gene
expression data obtained using the Lymph Dx microarray. This
predictor incorporated lymph node, germinal center B cell, and MHC
class II gene expression signatures. Fitting the Cox proportional
hazards model to the gene expression signature values obtained from
these signatures resulted in the following model:
Survival predictor score=[-0.32*(lymph node gene expression
signature value)]-[0.176*(germinal center B-cell gene expression
signature value)]-[0.206*(MHC class II gene expression signature
value)].
[0101] A method of refining a DLBCL survival predictor was
developed based on analysis of characteristic chromosomal
alterations in DLBCL cases. Malignant lymphomas are generally
characterized by distinctive recurrent primary chromosomal
translocations such as the t(11;14) or t(14;18), in MCL and PL,
respectively. By identifying genomic imbalances, comparative
genomic hybridization (CGH) has the potential to detect less
well-characterized chromosomal aberrations in lymphomas that may
play an important role in development and progression of the
disease, in DLBCL, previous cytogenetic studies have identified a
plethora of clonal chromosomal aberrations, some of which are
associated with particular morphological or clinical manifestations
(Yunis 1989; Monni 1996; Rao 1998; Cigudosa 1999; Schlegelberger
1999; Berglund 2002; Dave 2002; Nanjangud 2002; Bea 2004).
[0102] CGH was used to identify chromosomal alterations n 224 DLBCL
samples that had previously been broken into subtypes based on gene
expresslon data obtained using a Lymphochip microarray. Chromosomal
alterations were observed in 164 of the 224 cases. Certain
alterations were differentially distributed among subtypes. For
example, gains of chromosome arm 3q were observed in around a
fourth of ABC samples, but were never observed in GCB samples and
were observed only once in PMBL samples. Similarly, gains of
18q21-q22 were observed in around a third of ABC samples, but were
observed in only 10% and 16% of GCB and PMBL samples, respectively.
Genomic gains of 3q and 18q have previously been correlated with
shorter survival in DLBCL patients (Bea 2004). The present findings
provide a clear explanation for this observation, namely that both
abnormalities are statistically associated with ABC, which has a
worse prognosis than other DLBCL subtypes (Alizadeh 2000; Rosenwald
2002; Rosenwald 2003b). Alternatively, these genetic alterations
may themselves contribute at least in part to the ABC gene
expression phenotype and its inferior prognosis.
[0103] Other chromosomal abnormalities were found to occur more
frequently in one DLBCL subtype than another, but without being
restricted to a single subtype. For example, deletions of 6q21-q22
occurred in 40% was observed in 40% of ABC samples and 22% of GCB
samples, but never in PMBL samples. Gains and amplifications of
12cen-q15 were observed most frequently. In GCB samples, but were
also observed at a low frequency in both ABC and PMBL samples.
These results suggest that certain oncogenic pathways are shared by
various DLBCL subtypes, but nonetheless are more frequently
utilized in different subtypes.
[0104] The distinct patterns of genomic alterations observed across
different DLBCL subtypes are consistent with recent studies showing
a correlation between gene copy number changes and expression of
genes located within the involved genomic regions (Phillips 2001;
Vfrtaneva 2001; Hyman 2002; Pollack 2002; Orsetti 2004).
[0105] The relationship between chromosome gains/amplifications and
the expression profile of genes located within the gained/amplified
regions was examined by RQ-PCR for four chromosomal regions
commonly over represented in GCB and ABC tumors: 2p14-p16,
3q27-qter, 12q12-q15, and 18q21-q22. A strong impact of genomic
gain's and amplifications on gene expression was observed. 25-75%
of genes located within these chromosomal segments were
overexpressed in those tumors with increased DNA copy number.
[0106] For many genes, expression levels were significantly higher
in samples with gains or amplifications versus samples with normal
DNA profiles, which suggests a direct effect of copy number on mRNA
expression levels. However, not all genes in overrepresented
chromosomal regions were more highly expressed. This suggests that
either the individual genes were not amplified or that the
functional background of the cell was not appropriate for
expression of the gene. For example, REL was significantly
overexpressed in GGB samples with overrepresentation of 2p14-p16,
but not in ABC samples with overrepresentation of this region.
Quantitative PCR analysis confirmed that the REL locus was
amplified in virtually all GCB samples with overrepresentation of
the 2p14-p16 region. However, REL was not amplified in any of the
ABC samples with gains or amplifications of 2p14-p16, indicating
that genes other than REL may be targeted by 2p14-p16 gains in ABC.
Interestingly, mRNA expression of BCL11A, which is located very
close to REL, was not influenced by 2p14-p16 gains in GCB or ABC
samples, despite the fact that quantitative PCR analysis showed
amplification and gains of the BCL11A locus in both subtypes.
[0107] Gene expression studies showed that chromosomal alterations
in DLBCL cases are correlated with expression of certain gene
expression signatures. Unexpectedly, this correlation was seen not
only in gene expression signatures that reflect variation within
malignant cells (proliferation and MHC class II signatures), but
also in gene expression signatures that reflect the nature of
non-malignant DLBCL tumors (T cell and lymph node signatures). The
proliferation signature, which is more highly expressed in
proliferating than in quiescent cells, was increased in DLBCL
samples with genomic loss in 6q21 and gains in several bands of
chromosome 3. The MHC class II signature, which reflects the
coordinate regulation of all MHC class II genes in malignant DLBCL
cells, was decreased in DLBCL samples with gains of 3p11-p12. The T
cell signature, which reflects the infiltration of tumors by T
cells, was decreased in DLBCL samples with gains of cytobands in
chromosomes 7, 11, 12, and X or losses in 6q and 17p. The lymph
node signature, which reflects a host response characterized by
abundant expression of extracellular matrix components and
infiltration of tumors with immune cells other than T cells, was
increased in DLBCL samples with Xp21 gains and decreased in samples
with gains in several cytobands of chromosome 3.
[0108] Previous studies have suggested that specific genetic
alterations are relevant to predicting survival in DLBCL cases
(Yunls 1989; Bea 2004). However, the present study shows that only
gains in certain regions of chromosome 3 are significantly
associated with inferior survival after-adjusting for multiple
variable comparisons. Specifically, gains involving 3p11-p12 were
found to have prognostic value that was statistically independent
of previously defined DLBCL survival predictors based on optimal
gene expression-based models (Rosenwald 2002). This information can
be used to create a refilled DLBCL survival predictor. For example,
a survival predictor score may be calculated using an equation such
as:
Survival predictor score=[0.241*(proliferation gene expression
signature value)]+[0.310*(BMP6 expression value)]-[0.290*(germinal
center B cell gene expression signature value)]-[0.311*(MHC class
II gene expression signature value)]-[0.249*(lymph node gene
expression signature value)9 .
[0109] wherein a higher survival predictor score is associated with
worse survival. The DLBCL sample may then be assayed for gains or
amplifications in the 3p11-p12 using any method, such as for
example CGH. The identification of such gains or amplifications
corresponds;tq a decrease. In survival, and may be used to adjust
the survival predictor score accordingly. Alternatively,
identification of a gain or amplification of 3p11-p12 may be used
as a stand-alone indicator of worse survival for a DLBCL patient in
the absence of additional gene expression data.
[0110] An MCL survival predictor was generated using gene
expression data obtained using Affymetrix U133A, Asymetrix U133B,
and Lymph Dx microarrays. This predictor incorporated a
proliferation gene expression signature. Fitting the Cox
proportional hazards model to the gene expression signature values
obtained from these signatures resulted in the following model;
Survival predictor score=[1.66*(proliferation gene expression
signature value)].
[0111] Gene expression data can also be used to diagnose and
identify lymphoma types. In an embodiment of the present invention,
a statistical method based on Bayesian analysis was developed to
classify lymphoma specimens according to their gene expression
profiles. This method does not merely assign a tumor to a
particular lymphoma type, but also determines the probability that
the tumor belongs to that lymphoma type. Many different methods
have been formulated to predict cancer subgroups (Golub 1999;
Ramaswamy 2001; Dudolt 2002; Radmacher 2002). These methods assign
tumors to one of two subgroups based on expression of a set of
differentially expressed genes. However, they do not provide a
probability of membership in a subgroup. By contrast, the method
disclosed herein used Bayes' rule to estimate this probability,
thus allowing one to vary the probability cut-off for assignment of
a tumor to a particular subgroup. In tumor types in which unknown
additional subgroups may exist, the present method allows samples
that do not meet the gene expression criteria of known subgroups to
fall into an unclassified group with intermediate probability. A
cancer subgroup predictor of the type described herein may be used
clinically to provide quantitative diagnostic information for an
individual cancer patient. This information can in turn be used to
provide a predictor of treatment outcome for a particular cancer
patient.
[0112] For any two lymphoma types A and B, there is a set of genes
with significantly higher expression in type A than type B, and a
set of genes with significantly lower expression in type A than in
type B. By observing the expression of these genes in an unknown
sample, it is possible to determine to which of the two types the
ample belongs. Evaluating the likelihood that a particular sample
belongs to one or the other lymphoma type by Bayesian analysis may
be done using the following steps: [0113] 1. Identify those genes
that are most differentially expressed between the two lymphoma
types. This can be done by selecting those genes with the largest
t-statistic between the two lymphoma types. The genes in this step
may be subdivided into gene expression signatures in certain cases,
with genes from each signature analyzed separately. [0114] 2.
Create a series of linear predictor score (LPS) for samples
belonging to either lymphoma type. [0115] 3. Evaluate the LPS for
each sample in a training set, and estimate the distribution of
these scores within each lymphoma type according to a normal
distribution. [0116] 4. Use Bayes' rule to evaluate the probability
that each subsequent sample belongs to one or the other lymphoma
type. If only two types of lymphoma are being distinguished, then a
single probability score is sufficient to discriminate between the
two types. However, if more than two lymphoma types are being
distinguished, multiple scores will be needed to highlight specific
differences between the types.
[0117] A novel microarray termed the Lymph Dx microarray is
disclosed herein for the identification and diagnosis of various
lymphoma types. The Lymph Dx microarray contains cDNA probes
corresponding to approximately 2,653 genes, fewer than the number
seen on microarrays that have been used previously for lymphoma
diagnosis. The reduced number of probes on the Lymph Dx microarray
is the result of eliminating genes that are less useful for the
identification of lymphoma types and predicting clinical outcome.
This reduction allows for simplified analysis of gene expression
data. The genes represented on the Lymph Dx microarray can be
divided into four broad categories: 1,101 lymphoma predictor genes
identified previously using the Affymetrix U133 microarray, 171
outcome predictor genes, 167 new genes not found on the Affymetrix
U133 microarray, and 1,121 named genes. A list of the probe sets on
the Lymph Dx microarray is presented in Table 2, contained in the
file "Table_0002_LymphDx_Probe_List.txt."
[0118] Gene expression data obtained using the Lymph Dx microarray
may be used to identify and classify lymphomas using Bayesian
analysis using a strategy similar to that set forth above. In
certain embodiments, this strategy may include additional steps
designed to optimize the number of genes used and the cut-off
points between lymphoma types. A general overview of such a method
is presented in FIG. 1. Each gene represented on the Lymph Dx
microarray was placed into one of three gene-list categories based
on its correlation with the lymph node or proliferation gene
expression signatures: lymph node, proliferation, or standard.
These signatures were identified by clustering of the DLBCL cases
using hierarchical clustering and centroid-correlation of 0.35.
Standard genes were those with expression patterns that did not
correlate highly with expression of the lymph node or proliferation
signatures. Lymph Dx gene expression data was first used to
identify samples as FL, MCL, SLL, FH, or DLBCL/BL, then to identify
DLBCL/BL samples as ABG, GCB, PMBL, or BL. For each stage, a series
of pair-wise models was created, with each model containing a
different pair of lymphoma types (e.g:, FL vs. MCL, SLL vs. FH,
etc.). For each pair, the difference in expression of each gene on
the microarray was measured, and a t-statistic was generated
representing this difference. Genes from each gene-list category
were ordered based on their t-statistic, and those with the largest
t-statistics were used to generate a series of LPSs for samples
belonging to either lymphoma type. The number of genes used to
generate the LPSs was optimized by repeating the calculation using
between five and 100 genes from each gene-list category. The number
of genes from each category used in the final LPS calculation was
that which gave rise to the largest difference in LPS between the
two lymphoma types. Once the number of genes in each gene-list
category was optimized, four different LPSs were calculated for
each sample. The first included genes from the standard gene-list
category only, the second included genes from the proliferation and
standard gene-list categories, the third included genes from the
lymph node and standard gene-list categories, and the fourth
included genes from all three categories. The probability q that a
sample X belongs to the first lymphoma type of a pair-wise model
can then be calculated using an equation:
q = .phi. ( LPS ( X ) ; .mu. ^ 1 , .sigma. ^ 1 ) .phi. ( LPS ( X )
; .mu. ^ 1 , .sigma. ^ 1 ) + .phi. ( LPS ( X ) ; .mu. ^ 2 , .sigma.
^ 2 ) ##EQU00002##
LPS(X) is the LPS for sample X, .phi.(x, .mu., .sigma.) is the
normal density function with mean .mu. and standard deviation
.sigma.. {circumflex over (.mu.)} and {circumflex over (.sigma.)},
are the mean and variance of the LPSs for samples belonging to the
first lymphoma type, and {circumflex over (.mu.)} and {circumflex
over (.sigma.)} are the mean and variance of the LPSs for samples
belonging to the second lymphoma type. Samples with high q values
were classified as the first lymphoma type, samples with low q
values were classified as the second lymphoma type, and samples
with middle range q values were deemed unclassified. To determine
the proper cut-off point between high, low, and middle q values,
every possible cut-off point between adjacent samples was analyzed
by an equaltion:
3.99*[(% of type 1 misidentified as type 2)+(% of type 2
misidentified as type 1)]+[(% of type 1 unclassified)+(% of type 2
misidentified)].
This equation was used to favor the assignment of a sample to an
"unclassified" category rather than to an incorrect lymphoma type.
The final cut-off points were those which minimized this equation.
The coefficient of 3.99 was chosen arbitrarily to allow an
additional classification error only if the adjustment resulted in
four or more unclassified samples becoming correctly classified.
The coefficient can be varied to achieve a different set of
trade-offs between the number of unclassified and unidentified
samples.
[0119] To ensure that the accuracy of the model was not a result of
overfitting, each model was validated by leave-one-out
cross-validation. This entailed removing each sample of known
lymphoma type from the data one at a time, and then determining
whether the model could predict the missing sample. This process
confirmed the accuracy of the prediction method.
[0120] Bayesian analysis has been used herein to classify lymphoma
samples as DLBCL or BL based on gene expression data. BL is
characterized by a high degree of proliferation and deregulation of
the c-myc gene (Jaffe 2001). The diagnostic distinction between BL
and DLBCL is critically important because there are significant
differences in their clinical management. Lower-dose chemotherapy
regimens typically used to treat DLBCL (e.g.. CHOP) are not
adequate to treat BL (Bishop 2000; Butler 1993), which requires
intensive chemotherapy regimens (Pees 1992; Magrath 1996; Thomas
1999; Mead 2002; Divine 2005). Furthermore, prophylactic
intrathecal chemotherapy or systemic chemotherapy that crosses the
blood-brain barrier, which are unnecessary in most cases of DLBCL,
are essential in the treatment of BL due the high risk of central
nervous system involvement (Soussain 1995; Bishop 2000).
[0121] The diagnosis of BL relies on morphology, immunophenotype,
and cytogenetics (Jaffe 2001). However, DLBCL and BL can have
overlapping morphology and immunophenotype, and the characteristic
t(8;14) translocation of BL (Neri 1988; Gerbitz 1999; Hecht 2000)
is also found in 5-10% of DLBCL cases (Kramer 1998). Since DLBCL is
over 20 times more common than BL (Morton 2005), most aggressive
lymphomas with t(8;14) are not BL. Thus, the distinction between BL
and DLBCL can be difficult and may lead to incorrect clinical
decisions and adverse outcomes.
[0122] The term Burkitt-like lymphoma has been used to refer to
cases that have some features in common with BL. However, the most
recent WHO guidelines (Jaffe 2005) have eliminated Burkitt-like
lymphoma as a separate diagnostic category. Burkitt-like lymphoma
is now synonymous with the term atypical BL, which is reserved for
those cases that share the genetic abnormality and immunophenotype
of BL but have atypical morphology. It is not clear whether
atypical BL is biologically difference from BL or if it merely
represents a morphologic variant.
[0123] A gene expression-based predictor of BL that diagnoses
classic BL with 100% accuracy and/distinguishes it from DLBCL has
been developed. Surprisingly, eight cases that were giyen a
pathological diagnosis of DLBCL were similar to BL by gene
expression and had other molecular and clinical characteristics of
BL.
[0124] Compared to DLBCL, BL was found to have high expression of
the c-myc target gene expression signature and the GC B cell gene
expression signature, and low expression of the NF-/.kappa.B target
gene expression signature and the MHC class I gene expression
signature. A number of aggressive lymphomas that had been
classified as DLBCL by an expert panel of hematopathologlsts (n=8)
were reclassified as BL based on gene expression analysis: All
eight of these cases had c-myc translocations and resembled BL with
respect to all four gene expression signatures that distinguished
BL from DLBCL, suggesting that these cases represent BL that cannot
be reliably diagnosed by current methods. Consistent with previous
studies (Butler 1993; Magrath 1996; Smeland 2004), patients
classified as BL by gene expression had poor outcome with lower
dose chemotherapy regimens, yet could be cured with intensive
regimes.
[0125] The translocation of the c-myc gene and its consequent
deregulation is a key oncogenic event in the genesis of BL and,
accordingly, expression of the c-myc target gene expression
signature distinguished BL from DLBCL. However, c-myc
translocations also occur in 5-10% of DLBCL. It is therefore
noteworthy that the gene expression-based predictor disclosed
herein did not classify any of six DLBCL cases bearing a c-myc
translocation as BL. Thus, c-myc deregulation by translocation and
the attendant overexpression of c-myc target genes are not
sufficient to create the phenotype of BL. Rather, it is likely that
additional differences in the molecular pathogenesis of BL and
DLBCL contribute to their clinical differences.
[0126] In keeping with this notion, BL and DLBCL were found to
differ in the expression of three gene expression signatures in
addition to the c-myc target gene signature. Both BL and GCB are
thought to originate from a germinal center B cell (Mann 1976;
Alizadeh 2000). Surprisingly, however, there were subsets of
germinal center B cell genes that were differentially expressed
between BL and GCB.
[0127] NF-/.kappa.B target genes were expressed at very low levels
in BL as compared to the DLBCL subtypes. These genes are also known
to be expressed at lower levels in GCB than in ABC and PMBL
(Rosenwald 2003b; Savage 2003; Feuerhake 2005; Lam 2005). However,
BL was found to express NF-.kappa.B target genes at levels even
lower than those of GCB. It is unclear at present whether this low
expression reflects differences in the malignant cells or in
tumor-infiltrating immune cells.
[0128] BL tumors expressed MHC class I genes at very low levels
compared with DLBCL tumors. Previous studies have documented the
loss of MHC class I molecules in some BL-derived cell lines (Voltz
1989), but the mechanism underlying this downmodulation is unclear
at present.
[0129] The gene expression signatures that distinguish BL and DLBCL
provide insight into the nine BL-discrepant cases that were
classified as BL by gene expression but DLBCL by the panel of
hematopathologists. The five BL-discrepant that were BCL2-negative
were indistinguishable from the BL-concordant cases in the
expression of all four gene expression signatures. Therefore, these
cases bear all the hallmarks of BL but cannot be distinguished
using current methodologies. Interestingly, BL-discrepant cases
that were BCL2-positive resembled the BL-concordant cases with
respect to three gene expression signatures, but had lower
expression of the BL-high GC B cell signature. This phenotype was
also observed in the BCL2-positive BL-concordant cases. Cases
carrying dual translocations t(8;14) and t(14;18) have been
described previously as having a very aggressive course and a poor
prognosis (Macpherson 1999). The data presented herein confirm that
CHOP-like regimens are not adequate to treat such patients.
[0130] The method of distinguishing BLand DLBCL disclosed herein
provides a more quantitative and reproducible diagnosis of BL than
is afforded by current methods based on morphology and
immunophenotype. Such a method is clinically important because BL
is a curable malignancy. Previous studies have shown that BL
patients treated with CHOP-like chemotherapy regimens fare
significantly worse than those who receive intensive regimens
(Butler 1993; Magrath 1996; Smeland 2004). The results disclosed
herein reveal that this also true for cases that were diagnosed as
DLBCL pathologically but as BL based on gene expression. Correct
identification of these cases will greatly enhance the formulation
of treatment options for these BL-discrepant patients.
[0131] The methods discussed herein for identifying and classifying
lymphoma subtypes have been used to identify and characterize cases
of cyclin D1-negative MCL. Cyclin D1 overexpression has generally
been considered essential to MCL pathogenesis, in fact, the current
WHO guidelines for diagnosing MCL rely on morphologic examination
and immunophenotyping, and require demonstration of cyclin D1
overexpression and/or the t(11;14)(q13;q32) for confirmation.
Several suspected cases of cyclin-D1 MCL have been identified in
recent studies, but these cases have been controversial and
difficult to substantiate. Most reported cases of cyclin
D1-negative MCL have been attributed to suboptimal immunostaining,
inadequate genetic or molecular analyses, or misdiagnosis.
[0132] Nevertheless, in a recent study of 99 lymphomas, seven cases
were identified that were morphologically consistent with MCL but
lacked cyclin D1 expression as measured by quantitative RT-PCR and
Lymphochip cDNA microarray analyses (Rosenwald 2003). Other than
cyclin D1, these cases exhibited characteristic MCL gene expression
signatures as determined by cDNA microarray analysis, and were
therefore classified as cyclin D1-negative MCL. One of these seven
cases had the characteristic t(11;14)(q13;q32) as determined by
FISH analysis, and expressed cyclin D1 as determined by
immunohlstochemical staining. Thus, this case was determined to be
a false negative and was reclassified as cyclin D1-positive MCL.
Additional gene expression profiling analysis was performed using
U133A/B microarrays, and the algorithm for diagnosing MCL was
refined. Using this refined algorithm, four of the six remaining
cyclin D1-negative cases were determined to be unclassifiable
B-cell lymphomas, and were thus excluded from additional study. The
two remaining cases and four newly identified cases were used for
the current studies.
[0133] The present disclosure confirms and extends previous
findings regarding the identification of cyclin D1-negative MCL.
Six cases of MCL have been confirmed herein as negative for cyclin
D1 mRNA expression by quantitative RT-PCR, microarray analysis, and
immunostaining. These cases also lack the characteristic IGH/CCND1
fusion by FISH analysis. Nonetheless, all six cases exhibit the
characteristic pathologic features of MCL and, more importantly,
shared the characteristic MCL gene expression profile by microarray
analysis. Therefore, these cases are regarded as bona fide cases of
cyclin D1-negative MCL. The existence of such cases sheds new light
on the pathobiology of MCL and challenges the idea that cyclin D1
overexpression is essential to MCL pathogenesis. It is also shown
herein that patients with cyclin D1-negative MCL have clinical and
pathologic features similar to those with cyclin D1-positive MCL.
In particular, tumors in both groups have similar growth patterns
and common cytological and immunohistochemical features. Similar
age and sex distribution, stage, serum LDH levels, extranodal
sites, IPI scores, response to initial treatment, and overall
survival are observed in the cyclin D1-positive and cyclin
D1-negative groups.
[0134] Recent studies have reported 23 cyclin D1-negative cases
among 151 cases of lymphoma with the morphological features of MCL
based on immunohistochemical staining (Yatabe 2000). Conventional
cytogenetics was performed on only three of these 23 cases, and all
three were negative for the t(11;14)(q13;q32). However, FISH or
quantitative RT-PCR analysis was not performed on any of these
cases. Compared to the 128 cyclin D1-positive MCL cases, the 23
cyclin D1-negative cases exhibited significantly better overall
survival. Another recent study identified three cases of apparent
cyclin D1-negative MCL by immunostains and compared them to 14
cases of typical cyclin D1-positive MCL (Hashimoto 2002). This
study suggested that cyclin D1-negative MCL is a more indolent form
of MCL. However, neither of these studies provided convincing
evidence that the cyclin D1-negative MCL disclosed therein were
true cases of MCL. In fact, the Yatabe et al. study notes that some
of the cases identified as cyclin D1-negative MCL might actually be
marginal zone B-cell lymphomas or atypical small lymphocytic
lymphomas (Yatabe 2000). The results presented herein represent the
first demonstration of characteristic MCL gene expression signature
in a set of cyclin D1-negative MCL cases. No significant difference
in clinical features was identified between these cases and cyclin
D1-positive MCL.
[0135] The pathogenic mechanisms involved in the development of the
cyclin D1-negative MCL are currently unknown. Since the oncogenic
effect of overexpressed cyclin D1 is considered to be cell cycle
deregulation, other proteins involved in cell cycle control,
especially the G1 to S phase transition, were examined. The D-type
cyclins, D1, D2 and D3, are all positive promoters of cell cycle
progression from the G1 to S phase. The D-type cyclins are similar
in structure and biochemical function (In aba 1992), but are
expressed in a lineage-specific manner (Sherr 1994). There is
considerable redundancy in the growth promoting function af the
D-type cyclins, since only limited phenotypic consequences due to
the absence of either cyclin D1, D2, or D3 are seen in gene
knock-out mice (Sicinski 1995; Stcinskl 1996; Ciemerych 2002;
Sicinska 2003). In non-neoplastic lymph nodes and tonsils, cyclin
D2 is found mainly in intermolecular T-cells, whereas cyclin D3 is
found in centroblasts in lymphoid follicles and in scattered B
cells and T cells of the interfollicular areas (Teramoto 1999).
However, cyclin D1 is not expressed in non-neoplastic T-cells or
B-cells (Rosenberg 1991; Yang 1994). In low-grade B-cell
malignancies, overexpression of cyclin D2 mRNA was observed by
Northern blot analysis in 29 of 34 CLL cases and in all seven LPC
cases, but not in two cases of MCL (Delmer 1995). Cyclin D3 appears
tobe expressed more ubiquitously in B-cell malignancies, including
FL, marginal zone lymphoma, and DLBCL (Ciemerych 2002), but is
usually not expressed in lymphoid malignancies with either cyclin
D1 or D2 overexpression (Ott 1997; Doglioni 1998; Suzuki 1999). In
the current study, overexpression of either cyclin D2 or D3 was
observed in all six cases of cyclin D1-negative MCL, indicating an
important substitute role for these cyclins in the pathogenesis of
cyclin D1-negative MCL. However, the mechanism of cyclin D2 or D3
up-regulation in these cases remains unclear. No chromosomal
translocations or gene amplifications involving the cyclin D2 or D3
gene loci by FISH analysis were identified in these cases. The
findings herein are consistent with several previous studies which
suggested that deregulation of cyclin D2 or D3 expression is often
due to epigenetic mechanisms (Andreasson 1998; Bergsagel 2003;
Pruned 2003).
[0136] Deregulation of other genes or factors important in cell
cycle control could also play a role in the pathogenesis of such
cases. These may include deregulation of p27.sup.Klp1,
up-regulation of cyclin E, inactivation of the RB gene, deletion of
the p16INK4a/p14.sup.ARF locus, as well as involvement of other
genes. The p27.sup.Klp1 protein regulates cellular progression from
G1 into S phase by inhibiting the cyclin E/CDK2 complex (Polyak
1994). Regulation of p27.sup.Klp1 occurs primarily through
posttranscriptional mechanisms, including sequestration by cyclin
D1 or cyclin D3 (Lin 2003; Quintanilla-Martinez 2003) or
proteasomal degradation (Chlarle 2000). In a prior study,
expression of p27.sup.Klp1 as assessed by immunostains was noted in
only five of 40 cases of typical MCL, but was found in eight of ten
cases of blastic MCL (Quintanilla-Martinez 1998). In the current
study, down-regulation of p27.sup.Klp1 protein expression was seen
in all six cases, similar to that seen in typical cyclin
D1-positive MCL.
[0137] The E-type cyclins, including cyclin E1 and E2, are also
important in the G1 phase of the cell cycle. When combined with
CDK2, cyclin E promotes the hyper-phosphorylation of RB protein,
and thereby facilitates the entry of cells into S phase (Sherr
1996). However, none of the present cases were positive for cyclin
E expression, arguing against a role for cyclin E in the
pathogenesis of cyclin D1-negative MCL. In activation of the RB
tumor suppressor gene has been implicated in the development of
various types of human malignancy. However, RB protein expression
was identified in all of our cases and the expression levels were
similar to those seen in cyclin D1-positive MCL. The present
findings are consistent with a previous study concluding that RB
protein appears to be normally regulated in MCL (Jares 1996). The
present study also investigated whether deletions of the tumor
suppressor genes p16.sup.INKA8 and p14.sup.ARF play a role in
cyclin D1-negative MCL. p16.sup.INK4a regulates the G1/S phase
transition by forming binary complexes with CDK 4 and 6, thereby
preventing these subunits from association with D-type cyclins
(Sherr 2002). Deletion of p16.sup.INK4a or cyclin D1 overexpression
may therefore promote the G1/S phase transition by the same
mechanism. An important function of p14.sup.ARF is to augment p53
function by antagonizing MDM2, and loss of p14.sup.ARF function may
contribute to the enhanced proliferation in tumor cells (Sherr
2002). As has been shown previously, INK4a/ARF locus deletions
occur in up to 21% (18/85) cases, of MCL and are preferentially
observed among the more proliferative cases (Rosenwald 2003).
However, deletion of the INK4a/ARF locus was not identified in any
of the six cases, arguing against a role for
p16.sup.INK4a/p14.sup.ARF in the pathogenesis of cyclin D1-negative
MCL.
[0138] The classification of a lymphoproliferative disorder in
accordance with embodiments of the present invention may be used in
combination with any other effective classification feature or set
of features. For example, a disorder may be classified by a method
of the present invention in conjunction with WHO suggested
guidelines, morphological properties, histochemical properties,
chromosomal structure, genetic mutation, cellular proliferation:
rates, immunoreactivlty, clinical presentation, and/or response to
chemical, biological, or other agents. Embodiments of the present
invention may be used in lieu of or in conjunction with other
methods for lymphoma diagnosis, such as immunohistochemistry, flow
cytometry, FISH for translocations, or viral diagnostics.
[0139] Accurate determination of lymphoma type in a subject allows
for better selection and application of therapeutic methods.
Knowledge about the exact lymphoma affecting a subject allows a
clinician to select therapies or treatments that are most
appropriate and useful for that subject, while avoiding therapies
that are nonproductive or even counterproductive. For example, CNS
prophylaxis may be useful for treating BL but not DLBCL, CHOP
treatment may be useful for treating DLBCL but not biastic MCL
(Fisher 1993; Khourl 1998), and subjects with follicular lymphoma
frequently receive treatment while subjects with follicular
hyperplasia do not. In each of these situations, the lymphoma types
or subtypes in question can be difficult to distinguish using prior
art diagnostic methods. The diagnostic and identification methods
of the present invention allow for more precise delineation between
these lymphomas, which simplifies the decision of whether to pursue
a particular therapeutic option. Likewise, the survival prediction
methods disclosed in the present invention also allow for better
selection of therapeutic options. A subject with a very low
survival predictor score (i.e., very good prognosis) may not
receive treatment, but may instead be subjected to periodic
check-ups and diligent observation. As survival predictor scores
increase (i.e., prognosis gets worse), subjects may receive more
intensive treatments. Those subjects with the highest survival
predictor scores (i.e., very poor prognosis) may receive
experimental treatments or treatments with novel agents. Accurate
survival prediction using the methods disclosed herein provides an
improved tool for selecting treatment options and for predicting
the likely clinical outcome of those options.
[0140] Any effective method of quantifying the expression of at
least one gene, gene set, or group of gene sets may be used to
acquire gene expression data for use in embodiments of the present
invention. For example, gene expression data may be measured or
estimated using one or more microarrays. The microarrays may be of
any effective type, including but not limited to nucleic acid based
or antibody based. Gene expression may also be measured by a
variety of other techniques, including but not limited to PCR,
quantitative RT-PCR, real-time PCR, RNA amplification, in situ
hybridization, immunohistochemistry, immunocytochemistry, FACS,
serial analysis of gene expression (SAGE) (Velcufescu 1995),
Northern blot hybridization, or western blot hybridization.
[0141] Nucleic acid microarrays generally comprise nucleic acid
probes derived from individual genes and placed in an ordered array
on a support This support may be, for example, a glass slide, a
nylon membrane, or a silicon wafer. Gene expression patterns in a
sample are obtained by hybridizing the microarray with the gene
expression product from the sample. This gene expression product
may be for example, total cellular mRN A, rRNA, or cDNA obtained by
reverse transcription of total cellular mRNA. The gene expression
product from a sample is labeled with a radioactive, fluorescent,
or other label to allow for detection. Following hybridization, the
microarray is washed, and hybridization of gene expression product
to each nucleic acid probe on the microarray is detected and
quantified using a detection device such as a phosphorimager or
scanning confocal microscope.
[0142] There are two broad classes of microarrays: cDNA and
oligonucleotide arrays. cDNA arrays consist of hundreds or
thousands of cDNA probes immobilized on a solid support. These cDNA
probes are usually 100 nucleotides or greater in size. There are
two commonly used designs for cDNA arrays. The first is the
nitrocellulose filter array, which is generally prepared by robotic
spotting of purified DNA fragments or lysates of bacteria
containing cDNA clones onto a nitrocellulose filter (Southern 1992;
Southern 1994; Gress 1996; Pietu 1996). The other commonly used
cDNA arrays is fabricated by robotic spotting of PCR fragments from
cDNA clones onto glass microscope slides (Schena 1995; DeRisi 1996;
Schena 1996; Shalon 1996; DeRisi 1997; Heller 1997; Lashkari 1997).
These cDNA microarrays are simultaneously hybridized with two
fluorescent cDNA probes, each labeled with a different fluorescent
dye (typically Cy3 or Cy5). In this format, the relative mRNA
expression in two samples is directly compared for each gene on the
microarray. Oligonucleotide arrays differ from cDNA arrays in that
the probes are 20- to 25-mer oligonucleotides. Oligonucleotide
arrays are generally produced by in situ oligonucleotide synthesis
in conjunction with photolithographic masking techniques (Pease
1994; Upshutz 1995; Chee 1996; Lockhart 1996; Wodlcka 1997). The
solid support for oligonucleotide arrays is typically a glass or
silicon surface.
[0143] Methods and techniques applicable to array synthesis and use
have been described in, for example, U.S. Pat. No. 5,143,854
(Plrrung), U.S. Pat. No. 5,242,974 (Holmes), U.S. Pat. No.
5,252,743 (Barrett), U.S. Pat. No. 5,324,633 (Fodor), U.S. Pat. No.
5,384,261 (Winkler), U.S. Pat. No. 5,424,186 (Fodor), U.S. Pat. No.
5,445,934 (Fodor), U.S. Pat. No. 5,451,683 (Barrett), U.S. Pat. No.
5,482,867 (Barrett), U.S. Pat. No. 5,491,074 (Aldwin), U.S. Pat.
No. 5,527,681 (Holmes), U.S. Pat. No. 5,550,215 (Holmes), U.S. Pat.
No. 5,571,639 (Hubbell), U.S. Pat. No. 5,578.832 (Trulson), U.S.
Pat. No. 5,593,839 (Hubbell), U.S. Pat. No. 5,599,695 (Pease), U.S.
Pat. No. 5,624,711 (Sundberg), U.S. Pat. No. 5,631,734 (Stern),
U.S. Pat. No. 5,795,716 (Chee), U.S. Pat. No. 5,831,070 (Pease),
U.S. Pat. No. 5,837,832 (Chee), U.S. Pat. No. 5,856,101 (Hubbell),
U.S. Pat. No. 5,858,659 (Sapolsky), U.S. Pat. No. 5,936,324
(Montagu), U.S. Pat. No. 5,968,740 (Fodor), U.S. Pat. No. 5,974,164
(Chee). U.S. Pat. No. 5,981,185 (Matson), U.S. Pat. No. 5,981,956
(Stern), U.S. Pat. No. 6,025,601 (Trulson), U.S. Pat. No. 6,033,860
(Lockhart), U.S. Pat. No. 6,040.193 (Winkler), U.S. Pat. No.
6,090,555 (Flekowsky), and U.S. Pat. No. 6,410.229 (Lockhart), and
U.S. Patent Application Publication No. 20030104411 (Fodor). Each
of the above patents and applications is incorporated by reference
herein in its entirety.
[0144] Microarrays may generally be produced using a variety of
techniques, such as mechanical or light directed synthesis methods
that incorporate a combination of photolithographic methods and
solid phase synthesis methods. Techniques for the synthesis of
microarrays using mechanical synthesis methods are described in,
for example, U.S. Pat. No. 5,384.261 (Winkler) and U.S. Pat. No.
6,040,193 (Winkler). Although a planar array surface is preferred,
the microarray may be fabricated on a surface of vlrtually any
shape, or even on a multiplicity of surfaces. Microarrays may be
nucleic acids on beads, gels, polymeric surfaces, fibers such as
fiber optics, glass or any other appropriate substrate. See, for
example, U.S. Pat. No. 5,708,153 (Dower); U.S. Pat. No. 5,770,358
(Dower); U.S. Pat. No. 5,789,162 (Dower); U.S. Pat. No. 5,800,992
(Fodor); and U.S. Pat. No. 6,040,193 (Winkler), each of which is
incorporated by reference herein in its entirety.
[0145] Microarrays may be packaged in such a manner as to allow for
diagnostic use, or they can be an all-inclusive device. See, for
example, U.S. Pat. No. 5,856,174 (Upshutz) and U.S. Pat. No.
5,922,591 (Anderson), both of which are incorporated by reference
herein in their entirety.
[0146] Microarrays directed to a variety of purposes are
commercially available from Asymetrix (Affymetrix, Santa Clara,
Calif.). For instance, these microarrays may be used for genotyping
and gene expression monitoring for a variety of eukaryotic and
prokaryote species.
[0147] The following examples are provided to better illustrate the
claimed invention and are not to be interpreted as limiting the
scope of the invention. To the extent that specific materials are
mentioned, it is merely for purposes of illustration and is not
intended to limit the invention. One skilled in the art may develop
equivalent means or reactants without the exercise of inventive
capacity and without departing froth the scope of the invention. It
will be understood that many variations can be made in the
procedures herein described while still remaining within the bounds
of the present invention. It is the intention of the inventors that
such variations are included within the scope of the invention.
EXAMPLES
Example 1
Collection and Analysis of Gene Expression Data Using Affymetrix
U133A and U133B Microarrays
[0148] 568 cell samples representing various forms of human
lymphoid malignancies were obtained by biopsy using known methods
described in the literature. The samples were reviewed by a panel
of hematopathologists and classified into the following lymphoma
types based on current diagnostic criteria:
[0149] 231 diffuse large B cell lymphomas (DLBCL)
[0150] 191 follicular lymphomas (FL)
[0151] 26 Burkitt lymphomas (BL)
[0152] 21 mantle cell lymphoma (MCL)
[0153] 18 follicular hyperplasias (FH)
[0154] 17 small cell lymphocytic lymphomas (SLL)
[0155] 16 mucosa-associated lymphoid tissue lymphomas (MALT)
[0156] 13 splenic lymphomas (Splenic)
[0157] 10 cyclin-D1 negative lymphomas with MCL morphology
(CD1negMCL)
[0158] 9 multiple myeloma (Mult_Wyeloma)
[0159] 6 lymphoplasmacytlc lymphomas (LPC)
[0160] 4 post-transplant lymphoproliferative disorders (PTLD)
[0161] 3 lymphoblastic lymphomas (Lymbl)
[0162] 3 nodal marginal zone lymphomas (NMZ)
The 231 DLBCL samples were subdivided into the following lymphoma
types based on gene expression (see below):
[0163] 88 germinal center B cell-like (GCB)
[0164] 78 activated B cell-like (ABC).
[0165] 33 primary mediastinal B cell lymphoma (PMBL)
[0166] 32 samples for which the subtype could not be determined
(UC_DLBCL)
The 16 MALT samples were subdivided into the following four group
based on tumor origin:
[0167] 9 from the gastric region (MALT_gastric)
[0168] 1 from the salivary gland (MALT_salivary)
[0169] 1 from the lung (MALT_lung)
[0170] b 1 from the tonsil (MALT_tonsil)
[0171] 4 of unknown origin (MALT_unk)
[0172] Each of the 568 cell samples was given a unique sample ID
number consisting of the lymphoma type followed by a unique
numerical identifier. For example. "ABC_304" refers to an ABC DLBCL
sample numbered 304. Cells were purified and RNA was isolated from
the purified cells according to known methods described in the
literature.
[0173] Aliquots of RNA from each sample were applied to Affymetrix
U133A and Affymetrix U133B microarrays according to standard
Affymetrix protocol. The U133A and U133B microarrays are divided
into probe sets, with each probe set consisting of up to 69
oligonucleotide probes 25 nucleotides in length. Each probe set
represents a distinct human gene. Information pertaining to these
microarrays is available at www.affymetrix.com. Each microarray was
scanned using an Affymetrix scanner; which records signal intensity
for every probe on the microarray. This information can be
transformed into summary signal values for each probe set using a
number of different algorithms, including MAS 5.0, D-chip (Li
2001), or Bloconductor's RMA algorithms (Irlzarry 2003). The images
produced by the scanner were evaluated by Affymetrix MAS 5.0
software and stored as tables in .txt format. Since each sample was
scanned on both microarrays, there are two .txt files for each
sample. Each .txt file was given a unique name consisting of the
table number, sample ID number (discussed above), and a letter
denoting the microarray used. For example, Table_0588_ABC_304_A.txt
is the .txt file for Table 588, which contains data for sample ID
number ABC_304 from the U133A array. The data for each sample
tested is contained in Tables 3-1138.
[0174] The signal value for each probe on the U133A and U133B
microarrays was normalized to a target value of 500, and the base-2
log of the normalized values was used for the following analyses.
Log-signal values for each probe set are presented in Tables
1139-1706, contained in files with the title format
"Table_No._NAME_log_signal.txt," where NAME refers to the sample ID
number (e.g., ABC_304). The first column provides the UNIQID for
the probe set, while the second column provides the log-signal
value.
[0175] Log-signal files were statistically analyzed using S+
software and the S+ subtype predictor script contained in the file
entitled "Subtype_Predictor.txt," located in the computer program
listing appendix contained on CD number 22 of 22. Although the
log-signal values were analyzed using S+ software and the above
algorithm, any effective software/algorithm combination may be
used. Tables 1707-1721 provide descriptive statistical
characteristics for each of the lymphoma types tested except for
CD1negMCL, non-gastric MALT, and UC_DLBCL. Table 1722 provides
statistical characteristics for all MALT samples combined, while
Table 1723 does likewise for all DLBCL samples.
[0176] The files containing Tables 1707-1723 have the title format
"Table_No._TYPE_Stats.txt," where TYPE refers to the lymphoma type.
Each row of these tables represents a particular probe set. The
first column of each table provides the UNIQID for the probe set,
while the second column provides the average log-signal for the
probe set over all samples of a particular lymphoma type. The third
column provides the log-fold change in expression of the probe set
between the lymphoma type in question and a second lymphoma type.
For example, if logfold.ABC.vs.GCB is -0.21 for gene X, expression
of gene X in the ABC samples is, on average, 0.86 (i.e.,
2.sup.-0.21) times greater than expression of gene X in the GCB
samples. The fourth column provides a two-sided P-value derived
from a t-test of the log signals of the two lymphoma types compared
in column three. If, for example, P.value.ABC.vs.GCB was 0.00001
for gene X, this would indicate that the observed difference in
expression of gene X between ABC and GCB would only occur
approximately one time in 100,000 if there was no actual difference
in gene X expression between the two lymphoma types. The remainder
of the columns can be read as pairs that repeat the pattern of
columns three and four, presenting the log-fold change and P-value
of the difference in expression of the probe set for the lymphoma
type in question versus all other lymphoma types being tested.
Tables 1710, 1715, and 1723 (corresponding to FL, MCL, and DLBCL,
respectively) contain two additional columns entitled
"TYPE_Cox_coefficient" and "TYPE_Cox_P_value." The content of these
columns Ia discussed in the following examples.
Example 2
Collection of Gene Expression Data Using the Novel Lymph Dx
Microarray
[0177] The novel Lymph Dx microarray contains cDNA probes
corresponding to approximately 2,734 genes. 174 of these are
"housekeeping" genes present for quality control, since they
represent genes that are most variably expressed across ell
lymphoma samples. Other genes represented on the microarray were
selected for their utility in identifying particular lymphoma
samples and predicting survival in those samples. The genes
represented on the Lymph Dx microarray can be divided into four
broad categories; 1,101 lymphoma predictor genes identified
previously using the Affymetrix U133 microarray, 171 outcome
predictor genes identified using the Affymetrix U133 microarray,
167 genes not found on the Affymetrix U133 microarray but
represented on the Lymphochip microarray (Alizadeh 1999), and 1,121
named genes. The types of genes making up each of these broad
categories are summarized in Table 1724, below, while the specific
genes represented on the Lymph Dx microarray are listed in Table 2,
contained in the file "Table_0002_LymphDx_Probe_List.txt."
TABLE-US-00002 TABLE 1724 Number of Gene type genes Lymphoma
predictor genes 1101 Subtype specific 763 Lymph node signature 178
Proliferation signature 160 Outcome predictor genes 171 DLBCL 79 FL
81 MCL 11 New genes not on U133 167 Lymphochip lymphoma predictor
genes 84 EBV and HHV8 viral genes 18 BCL-2/cyclin D1/INK4a
specialty probes 14 Named genes missing from U133 51 Named genes
1121 Protein kinase 440 Interleukin 35 Interleukin receptor 29
Chemokine 51 Chemokine receptor 29 TNF family 26 TNF receptor
family 51 Adhesion 45 Surface marker 264 Oncogene/tumor suppressor
49 Apoptosis 46 Drug target 10 Regulatory 46
[0178] Cell samples representing various forms of human lymphoid
malignancy were obtained by biopsy using known methods described in
the literature. These 634 biopsy samples were reviewed by a panel
of hematopathologlsts and classified into the following lymphoma
types based on current diagnostic criteria: [0179] 201 diffuse
large B-cell lymphomas(DLBCL) [0180] 191 follicular lymphomas (FL)
[0181] 60 Burtott lymphomas (BL) [0182] 21 mantle cell lymphomas
(MCL) [0183] 30 primary mediastinal B cell lymphoma (PMBL) [0184]
18 follicular hyperplasias (FH) [0185] 18 small cell lymphocytic
lymphomas (SLL) [0186] 17 mucosa-associated lymphoid tissue
lymphomas (MALT), including 9 gastric MALTs (GMALT) [0187] 16
chronic lymphocytic leukemias (CLL) [0188] 13 splenic lymphomas
(SPL) [0189] 11 lymphoplasmacytlc lymphomas (LPC) [0190] 11
transformed DLBCL (trDLBCL) (DLBCL that arosa from an antecedent
FL) [0191] 10 cyclin D1 negative lymphomas with MCL morphology
(CD1N) [0192] 6 peripheral T-cell lymphoma (PTCL) [0193] 4
post-transplant lymphoproliferative disorders (PTLD) [0194] 4 nodal
marginal zone lymphomas (NMZ) [0195] 3 lymphoblastic lymphomas
(LBL)
[0196] Each of the 634 samples was given a unique sample ID number
consisting of the lymphoma type followed by a unique numerical
identifier. For example, "BL_2032_52748" refers to a Burkitt
lymphoma sample with the numerical identifier 2032_52748. Cells
were purified and RNA was isolated from the purified cells
according to known methods described in the literature.
[0197] Aliquots of purified RNA from each sample were applied to
the Lymph Dx microarrays according to standard Affymetrix
microarray protocol. Each microarray was scanned on an Affymetrix
scanner. This scanner produced an image of the microarray, which
was then evaluated by Affymetrix MAS 5.0 software. This information
was stored in tables in .txt format. Each of these .txt files was
given a unique name consisting of the table number, the sample ID
number (discussed above), and the UNIQID for identifying the array
data in the National Cancer Institute Database. For example,
Table_1725_BL_2032_52748.txt is the .txt file for Table 1725, which
contains data for sample ID number BL_2032. The data for each
sample analyzed is contained in Tables 1725-2358. The signal
intensity for each probe on the microarray can be transformed into
summary signal values for each probe set through a number of
different algorithms, including but not limited to MAS 5.0, D-chip
(Li 2001), or Bioconductor's RMA algorithms (Irizarry 2003).
Example 3
Development of a First FL Survival Predictor Using Gene Expression
Data From Affymetrix U133A and U133B Microarrays
[0198] An analytical method entitled Survival Signature Analysis
was developed to create survival prediction models for lymphoma.
This method is summarized in FIG. 2. The key feature of this method
is the identification of gene expression signatures, Survival
Signature Analysis begins by identifying genes whose expression
patterns are statistically associated with survival. A hierarchical
clustering algorithm is then used to identify subsets of these
genes with correlated expression patterns across the lymphoma
samples. These subsets are operationally defined as
"survival-associated signatures." Evaluating a limited number of
survival-associated signatures mitigates the multiple comparison
problems that are inherent in the use of large-scale gene
expression data sets to create statistical models of survival
(Ransohoff 2004).
[0199] FL samples were divided into two equivalent groups: a
training set (95 samples) for developing the survival prediction
model, and a validation set (96 samples) for evaluating the
reproducibility of the model. The overall survival of this cohort
is depicted in FIG. 3. The median age at diagnosis was 51 years
(ranging from 23 to 81 years), and the patients had a median
follow-up of 6,6 years (8.1 years for survivors, with a range of
<1 to 28.2 years). Gene expression data from Affymetrix U133A
and U133B microarrays was obtained for each sample. Within the
training set, a Cox proportional hazards model was used to identify
"survival predictor" genes, which were genes whose expression
levels were associated with long survival (good prognosis genes) or
short survival (poor prognosis genes). A hierarchical clustering
algorithm (Eisen 1998) was used to identify gene expression
signatures within the good and poor prognosis genes according to
their expression pattern across all samples. Ten gene expression
signatures were observed within either the good prognosis or poor
prognosis gene sets (FIG. 4). The expression level of every
component gene in each of these ten gene expression signatures was
averaged to create a gene expression signature value.
[0200] To create a multivariate model of survival, different
combinations of the ten gene expression signature values were
generated and evaluated for their ability to predict survival
within the training set. Among models consisting of two signatures,
an exceptionally strong statistical synergy was observed between
one signature from the good prognosis group and one signature from
the poor prognosis group. These signatures were deemed "immune
response-1" and "immune response-2," respectively, based on the
biological function of certain genes within each signature. The
immune response-1 gene expression signature included genes encoding
T cell markers (e.g., CD7, CD8B1, ITK, LEF1, STAT4) and genes that
are highly expressed in macrophages (e.g., ACTN1, TNFSF13B). The
immune response-1 signature is not merely a surrogate for the
number of T cells in the FL biopsy sample because many other
standard T cell genes (e.g., CD2, CD4, LAT, TRIM, SH2D1A) were not
associated with survival. The immune response-2 gene expression
signature included genes known to be preferentially expressed in
macrophages and/or dendritic cells (e.g., TLR5, FCGR1A, SEPT10,
LGMN, C3AR1). Table 2359 lists the genes that were used to generate
the gene expression signature values for the immune response-1 and
immune response-2 signatures.
TABLE-US-00003 TABLE 2359 Unigene ID Build 167 (http://www.ncbi.-
nlm.nih.gov/ Signature UNIQID UniGene) Gene symbol Immune
response-1 1095985 83883 TMEPAI Immune response-1 1096579 117339
HCST Immune response-1 1097255 380144 Immune response-1 1097307
379754 LOC340061 Immune response-1 1097329 528675 TEAD1 Immune
response-1 1097561 19221 C20orf112 Immune response-1 1098152 377588
KIAA1450 Immune response-1 1098405 362807 IL7R Immune response-1
1098548 436639 NFIC Immune response-1 1098893 43577 ATP8B2 Immune
response-1 1099053 376041 Immune response-1 1100871 48353 Immune
response-1 1101004 2969 SKI Immune response-1 1103303 49605 C9orf52
Immune response-1 1107713 171806 Immune response-1 1115194 270737
TNFSF13B Immune response-1 1119251 433941 SEPW1 Immune response-1
1119838 469951 GNAQ Immune response-1 1119924 32309 INPP1 Immune
response-1 1120196 173802 TBC1D4 Immune response-1 1120267 256278
TNFRSF1B Immune response-1 1121313 290432 HOXB2 Immune response-1
1121406 NA TNFSF12 Immune response-1 1121720 80642 STAT4 Immune
response-1 1122956 113987 LGALS2 Immune response-1 1123038 119000
ACTN1 Immune response-1 1123092 437191 PTRF Immune response-1
1123875 428 FLT3LG Immune response-1 1124760 419149 JAM3 Immune
response-1 1128356 415792 C1RL Immune response-1 1128395 7188
SEMA4C Immune response-1 1132104 173802 TBC1D4 Immune response-1
1133408 12802 DDEF2 Immune response-1 1134069 405667 CD8B1 Immune
response-1 1134751 106185 RALGDS Immune response-1 1134945 81897
KIAA1128 Immune response-1 1135743 299558 TNFRSF25 Immune
response-1 1135968 119000 ACTN1 Immune response-1 1136048 299558
TNFRSF25 Immune response-1 1136087 211576 ITK Immune response-1
1137137 195464 FLNA Immune response-1 1137289 36972 CD7 Immune
response-1 1137534 36972 CD7 Immune response-1 1139339 47099
GALNT12 Immune response-1 1139461 14770 BIN2 Immune response-1
1140391 44865 LEF1 Immune response-1 1140524 10784 C6orf37 Immune
response-1 1140759 298530 RAB27A Immune response-2 1118755 127826
EPOR Immune response-2 1118966 19196 LOC51619 Immune response-2
1121053 1690 FGFBP1 Immune response-2 1121267 334629 SLN Immune
response-2 1121331 8980 TESK2 Immune response-2 1121766 396566 MPP3
Immune response-2 1121852 421391 LECT1 Immune response-2 1122624
126378 ABCG4 Immune response-2 1122679 232770 ALOXE3 Immune
response-2 1122770 66578 CRHR2 Immune response-2 1123767 1309 CD1A
Immune response-2 1123841 389 ADH7 Immune response-2 1126097 498015
Immune response-2 1126380 159408 Immune response-2 1126628 254321
CTNNA1 Immune response-2 1126836 414410 NEK1 Immune response-2
1127277 121494 SPAM1 Immune response-2 1127519 NA Immune response-2
1127648 285050 Immune response-2 1128483 444359 SEMA4G Immune
response-2 1128818 115830 HS3ST2 Immune response-2 1129012 95497
SLC2A9 Immune response-2 1129582 272236 C21orf77 Immune response-2
1129658 58356 PGLYRP4 Immune response-2 1129705 289368 ADAM19
Immune response-2 1129867 283963 G6PC2 Immune response-2 1130003
432799 Immune response-2 1130388 19196 LOC51619 Immune response-2
1131837 156114 PTPNS1 Immune response-2 1133843 6682 SLC7A11 Immune
response-2 1133949 502092 PSG9 Immune response-2 1134447 417628
CRHR1 Immune response-2 1135117 512646 PSG6 Immune response-2
1136017 1645 CYP4A11 Immune response-2 1137478 315235 ALDOB Immune
response-2 1137745 26776 NTRK3 Immune response-2 1137768 479985
Immune response-2 1138476 351874 HLA-DOA Immune response-2 1138529
407604 CRSP2 Immune response-2 1138601 149473 PRSS7 Immune
response-2 1139862 251383 CHST4 Immune response-2 1140189 287369
IL22 Immune response-2 1140389 22116 CDC14B
[0201] Although the immune response-1 and immune response-2 gene
expression signatures taken individually were not ideal predictors
of survival, the binary model formed by combining the two was more
predictive of survival in the training set than any other binary
model (p<0.001). Using this binary model as an anchor, other
signatures were added to the model using a step up procedure
(Drapner 1966). Of the remaining eight signatures, only one
signature contributed significantly to the model in the training
set (p<0.01), resulting in a three-variable model for survival.
This model was associated with survival in a highly statistically
significant fashion in both the training (p<0.001) and
validation sets (p=0.003). However, only the immune response-1 and
immune response-2 gene expression signatures contributed to the
predictive power of the model in both the training set and the
validation set. The predictive power of each of these signatures is
summarized in Table 2360.
TABLE-US-00004 TABLE 2360 Contribution of Relative risk of
signature to death among Effect of model in patients in increased
Gene expression validation set validation set expression on
signature (p-value) (95% C.I.) survival Immune response-1 <0.001
0.15 (0.05-0.46) Favorable Immune response-2 <0.001 9.35
(3.02-28.9) Poor
Based on this information, the third signature was removed from the
model and the two-signature model was used to generate a survival
predictor score using the following equation:
Survival predictor score=[(2.71*immune response-2 gene expression
signature value)]-[(2.36.times.immune response-1 gene expression
signature value)].
A higher survival predictor score was associated with worse
outcome. The two-signature model was associated with survival in a
statistically significant fashion in both the training set
(p<0.001) and the validation set (p<0.001), which
demonstrated that the model was reproducible. For the 187 FL
samples with available clinical data, the survival predictor score
had a mean of 1.6 and a standard deviation of 0.894, with each unit
increase in the predictor score corresponding to a 2.5 fold
increase in the relative risk of death. Data for all 191 samples is
shown in Table 2361.
TABLE-US-00005 TABLE 2361 Length of Status Immune Immune Survival
follow-up at response-1 response-2 predictor Sample ID # Set
(years) follow-up signature value signature value score FL_1073
Training 7.68 Dead 9.20 8.67 1.77 FL_1074 Training 4.52 Dead 9.10
8.57 1.74 FL_1075 Validation 4.52 Dead 8.97 8.69 2.38 FL_1076
Training 3.22 Dead 9.20 8.55 1.44 FL_1077 Training 7.06 Alive 9.80
8.46 -0.20 FL_1078 Training 4.95 Alive 9.32 8.23 0.30 FL_1080
Training 6.05 Alive 9.45 8.94 1.93 FL_1081 Validation 6.61 Alive
9.00 8.22 1.05 FL_1083 Training 10.01 Alive 9.82 8.72 0.47 FL_1085
Validation 8.84 Alive 9.31 8.58 1.29 FL_1086 Validation 1.98 Dead
9.49 9.09 2.22 FL_1087 Training 8.19 Alive 9.98 9.27 1.57 FL_1088
Validation 5.30 Alive 9.22 8.47 1.20 FL_1089 Training 10.72 Alive
9.42 8.35 0.40 FL_1090 Validation 10.20 Alive 9.27 8.37 0.82
FL_1097 Validation 8.79 Dead 9.87 8.92 0.87 FL_1098 Validation 5.34
Dead 9.33 8.81 1.87 FL_1099 Training 7.65 Alive 9.73 9.04 1.54
FL_1102 Validation 13.20 Dead 9.45 8.89 1.79 FL_1104 Training 8.42
Dead 9.30 8.27 0.48 FL_1106 Validation 7.94 Alive 9.13 9.19 3.36
FL_1107 Training 5.01 Dead 9.41 9.32 3.07 FL_1183 Training 11.56
Dead 9.31 8.53 1.16 FL_1184 Training 6.93 Dead 9.66 8.83 1.13
FL_1185 Validation 7.02 Dead 9.23 9.09 2.86 FL_1186 Training 1.34
Dead 9.01 8.84 2.68 FL_1416 Validation 6.21 Alive 9.50 8.67 1.08
FL_1417 Training 2.40 Dead 8.47 8.39 2.73 FL_1418 Validation 3.59
Alive 8.94 8.42 1.72 FL_1419 Training 3.85 Alive 9.82 8.56 0.03
FL_1422 Training 5.72 Alive 9.46 8.49 0.68 FL_1425 Validation 4.26
Alive 8.93 8.50 1.98 FL_1426 Training 7.32 Alive 9.08 8.26 0.97
FL_1427 Training 5.22 Alive 8.57 8.28 2.22 FL_1428 Validation 5.41
Dead 9.22 8.44 1.10 FL_1432 Training 3.68 Alive 9.22 8.95 2.51
FL_1436 Training 9.08 Dead 9.48 8.63 1.02 FL_1440 Training 7.85
Alive 9.07 8.35 1.22 FL_1445 Training 9.24 Dead 8.67 8.66 3.01
FL_1450 Validation 0.65 Dead 9.83 9.99 3.86 FL_1472 Validation
16.72 Alive 8.85 8.49 2.10 FL_1473 Training 15.07 Alive 9.75 8.50
0.02 FL_1474 Validation 2.75 Dead 9.34 9.10 2.62 FL_1476 Validation
4.08 Dead 9.51 8.87 1.60 FL_1477 Training 0.59 Dead 9.64 9.06 1.83
FL_1478 Training 12.47 Dead 9.60 8.87 1.39 FL_1479 Training 2.29
Dead 8.71 9.07 4.01 FL_1480 Training 16.29 Alive 9.40 6.67 1.30
FL_1579 Training 8.22 Dead 8.81 8.44 2.10 FL_1580 Training 19.30
Alive 9.58 8.52 0.49 FL_1581 Training 9.52 Dead 9.08 9.02 3.00
FL_1582 Validation 1.30 Dead 8.40 8.18 2.36 FL_1583 Training 15.26
Dead 9.47 8.79 1.48 FL_1584 Training 15.73 Dead 9.44 8.55 0.89
FL_1585 Validation 0.01 Alive 8.96 8.53 1.96 FL_1586 Validation
3.11 Alive 9.38 8.55 1.03 FL_1588 Training 0.49 Dead 9.52 9.06 2.08
FL_1589 Training 3.15 Alive 9.72 8.74 0.72 FL_1591 Training 11.22
Alive 9.49 8.62 0.97 FL_1594 Validation 11.19 Alive 9.25 8.59 1.47
FL_1595 Training 8.03 Alive 9.75 9.60 3.01 FL_1598 Validation 2.80
Dead 8.81 8.33 1.79 FL_1599 Validation 6.17 Alive 9.48 8.65 1.06
FL_1603 Training 5.17 Dead 9.66 9.75 3.63 FL_1604 Training 3.98
Dead 9.24 8.86 2.20 FL_1606 Validation 4.22 Dead 9.45 9.18 2.57
FL_1607 Validation 8.12 Alive 9.40 8.60 1.13 FL_1608 Validation
9.70 Alive 8.92 8.41 1.72 FL_1610 Validation 2.05 Dead 9.33 9.35
3.32 FL_1611 Validation 10.15 Alive 9.42 8.69 1.31 FL_1616 Training
2.36 Dead 9.38 8.82 1.78 FL_1617 Validation 7.85 Alive 8.96 8.49
1.87 FL_1619 Validation 9.24 Dead 9.43 8.56 0.94 FL_1620 Validation
9.36 Dead 9.14 8.35 1.04 FL_1622 Training 14.01 Alive 9.23 8.53
1.33 FL_1623 Training 9.72 Alive 9.67 8.93 1.38 FL_1624 Validation
3.98 Dead 9.05 8.50 1.70 FL_1625 Validation 11.16 Alive 8.98 8.47
1.75 FL_1626 Validation 6.47 Dead 8.59 8.14 1.76 FL_1628 Validation
0.82 Dead 9.80 8.72 0.51 FL_1637 Validation 18.81 Alive 9.95 9.58
2.48 FL_1638 Validation 4.06 Alive 9.13 8.88 2.51 FL_1639 Training
4.75 Alive 9.53 8.89 1.62 FL_1643 Training 0.77 Dead 9.73 9.06 1.58
FL_1644 Validation 3.84 Alive 9.55 8.68 0.98 FL_1645 Training 3.56
Alive 9.49 8.70 1.18 FL_1646 Training 1.97 Dead 9.25 8.61 1.50
FL_1647 Training 1.22 Dead 9.12 8.89 2.55 FL_1648 Training 11.01
Alive 9.13 8.12 0.46 FL_1652 Training 3.72 Dead 9.50 9.14 2.35
FL_1654 Validation 0.30 Dead 8.74 8.28 1.82 FL_1655 Training 8.45
Alive 9.51 8.85 1.53 FL_1656 Validation 9.36 Alive 9.06 8.58 1.87
FL_1657 Training 10.09 Alive 9.53 8.46 0.44 FL_1660 Training 2.32
Alive 8.81 8.38 1.91 FL_1661 Validation 1.48 Alive 9.86 8.90 0.85
FL_1662 Validation 0.74 Dead 9.57 9.15 2.21 FL_1664 Validation 4.53
Dead 9.34 8.62 1.31 FL_1669 Training 4.40 Dead 8.87 8.58 2.30
FL_1670 Training 1.88 Alive 9.64 9.45 2.86 FL_1675 Training 4.57
Alive 9.36 8.46 0.84 FL_1681 Validation 4.23 Alive 9.52 8.63 0.91
FL_1683 Validation 4.03 Dead 9.95 9.10 1.19 FL_1684 Training 2.88
Dead 9.53 8.73 1.18 FL_1716 Validation 9.69 Alive 8.95 8.35 1.50
FL_1717 Validation 2.01 Dead 9.35 8.88 1.98 FL_1718 Training 10.35
Alive 9.23 8.13 0.26 FL_1719 Validation 7.70 Dead 9.13 8.50 1.49
FL_1720 Training 3.91 Dead 8.78 8.88 3.33 FL_1729 Training 8.06
Alive 9.35 8.65 1.39 FL_1732 Validation 0.71 Dead 7.81 8.59 4.86
FL_1761 Validation 10.83 Alive 9.31 8.55 1.22 FL_1764 Training 0.42
Dead 9.25 8.87 2.21 FL_1768 Training 13.04 Alive 9.42 8.47 0.72
FL_1771 Training 9.26 Dead 9.09 8.67 2.06 FL_1772 Validation 13.64
Dead 9.49 8.49 0.61 FL_1788 Training 1.00 Dead 9.09 9.13 3.29
FL_1790 Training 1.42 Alive 9.85 9.40 2.22 FL_1792 Validation 2.01
Dead 9.33 8.72 1.61 FL_1795 Training 0.71 Dead 10.19 9.27 1.08
FL_1797 Validation 7.17 Alive 9.34 8.92 2.14 FL_1799 Training 14.18
Alive 9.32 8.63 1.38 FL_1810 Validation 9.91 Alive 8.66 8.41 2.35
FL_1811 Validation 3.04 Alive 9.38 8.27 0.29 FL_1825 Training 2.98
Alive 9.46 9.07 2.25 FL_1827 Training 3.66 Alive 9.80 8.84 0.83
FL_1828 Validation 11.51 Alive 8.99 8.09 0.72 FL_1829 Validation
4.11 Alive 9.57 8.73 1.08 FL_1830 Validation 5.65 Dead 9.01 8.68
2.25 FL_1833 Training 11.95 Alive 9.74 8.67 0.51 FL_1834 Validation
16.92 Alive 9.22 8.72 1.88 FL_1835 Validation 12.49 Alive 9.26 8.83
2.10 FL_1836 Validation 12.24 Alive 9.55 8.64 0.85 FL_1837
Validation 0.55 Dead 9.47 8.84 1.62 FL_1838 Validation 2.54 Alive
9.90 9.12 1.34 FL_1839 Training 4.48 Alive 8.56 8.32 2.34 FL_1841
Training 0.88 Dead 9.32 9.10 2.66 FL_1842 Validation 4.56 Alive
9.73 8.87 1.07 FL_1844 Validation 13.39 Alive 9.41 8.55 0.98
FL_1845 Training 12.92 Dead 9.89 9.04 1.16 FL_1846 Validation 1.80
Dead 9.79 9.61 2.93 FL_1848 Training 12.52 Alive 9.78 8.81 0.82
FL_1851 Training 4.08 Dead 9.43 9.01 2.18 FL_1853 Validation 12.50
Alive 9.28 8.54 1.25 FL_1854 Validation 13.81 Alive 9.32 8.84 1.98
FL_1855 Validation 9.96 Dead 9.31 8.39 0.75 FL_1857 Validation 8.39
Dead 9.80 9.14 1.65 FL_1861 Validation 8.18 Dead 9.47 8.57 0.88
FL_1862 Validation 7.22 Dead 8.98 8.33 1.44 FL_1863 Validation
10.77 Dead 9.31 8.86 2.00 FL_1864 Training 14.25 Alive 9.98 9.12
1.17 FL_1866 Training 10.72 Dead 9.93 8.94 0.79 FL_1870 Validation
6.41 Dead 10.01 9.22 1.36 FL_1873 Training 7.78 Dead 9.39 8.66 1.30
FL_1874 Validation 3.15 Dead 9.38 8.74 1.53 FL_1876 Validation
15.07 Alive 9.59 8.72 0.98 FL_1879 Training 7.13 Dead 9.25 8.62
1.53 FL_1880 Validation 12.84 Dead 8.82 8.35 1.82 FL_1882 Training
8.84 Dead 9.43 8.76 1.49 FL_1884 Validation 11.92 Dead 9.48 9.14
2.41 FL_1885 Validation 15.49 Alive 9.70 8.85 1.11 FL_1887 Training
5.14 Dead 9.47 8.57 0.87 FL_1888 Training 15.08 Alive 9.83 8.97
1.11 FL_1890 Training 3.03 Dead 9.29 9.05 2.60 FL_1894 Training
11.37 Dead 9.01 8.64 2.13 FL_1896 Training 12.03 Alive 9.80 8.56
0.08 FL_1897 Training 9.63 Alive 9.02 8.33 1.29 FL_1898 Training
5.20 Alive 8.82 8.25 1.54 FL_1900 Validation 7.38 Alive 9.13 8.26
0.85 FL_1903 Validation 28.25 Alive 9.07 8.46 1.54 FL_1904
Validation 7.36 Alive 9.16 8.53 1.50 FL_1905 Validation 3.68 Dead
9.25 8.38 0.87 FL_1906 Training 2.35 Dead 8.04 8.69 4.56 FL_1907
Validation 2.35 Dead 8.11 8.21 3.11 FL_1910 Training 13.84 Alive
9.36 8.72 1.56 FL_1912 Validation 0.73 Dead 9.30 9.21 3.02 FL_1913
Training 2.57 Alive 9.77 8.51 0.01 FL_1916 Validation 11.61 Alive
9.22 8.49 1.24 FL_1918 Validation 9.95 Dead 9.54 8.77 1.26 FL_1919
Training 10.84 Dead 9.51 8.81 1.44 FL_735 Validation 11.05 Dead
8.81 8.23 1.53 FL_738 Validation 10.15 Dead 9.19 8.79 2.13 FL_739
Training 10.80 Dead 9.29 8.77 1.85 FL_878 Validation 3.87 Dead 8.85
8.54 2.26 FL_879 Training 4.34 Dead 8.95 8.74 2.56 FL_886
Validation 3.29 Alive 9.43 8.72 1.40 FL_888 Validation 1.32 Dead
8.76 8.49 2.34 FL_1627 Training NA NA 9.60 8.51 0.40 FL_1429
Training NA NA 8.69 8.28 1.93 FL_1850 Validation NA NA 9.75 8.83
0.92 FL_1735 Validation NA NA 7.32 8.30 5.24
[0202] In order to visualize the predictive power of the model, the
FL samples were ranked according to their survival predictor scores
and divided into four quartiles, Kaplan-Meier plots of overall
survival showed clear differences in survival rate in the
validation set (FIG. 5). The median survival for each of the four
quartiles is set forth in Table 2362.
TABLE-US-00006 TABLE 2362 Quartile Median survival (years) 1 13.6 2
11.1 3 10.8 4 3.9
[0203] Various clinical variables were found to be significantly
associated with survival, including the IPI and some of its
components and the presence of B-symptoms. The gene
expression-based model was independent of each of these variables
at predicting survival. These clinical variables and the relative
risk of death associated with each are summarized in Table
2363.
TABLE-US-00007 TABLE 2363 Multivariate (clinical Univariate
(clinical variable + survival variable only) predictor score)
relative risk of death relative risk of death % of % of among
patients in among patients in patients.sup.1 patients.sup.1
validation set validation set Clinical Training Validation RR.sup.2
RR.sup.2 variable Criteria set set (95% C.I.) p-value (95% C.I.)
p-value Age 60 64.5 70.2 1.90 0.044 2.21 <0.001 >60 35.5 29.8
(1.02-3.56) (1.48-3.29) Stage I-II 33.3 25 1.31 0.447 2.31
<0.001 III-IV 66.7 75 (0.65-2.64) (1.61-3.52) Extranodal 2 5.4
20.2 1.58 0.163 2.21 <0.001 sites (#) <2 94.6 79.8
(0.83-2.99) (1.48-3.30) LDH Normal 77.1 66.2 1.77 0.065 2.40
<0.001 Greater 22.9 33.8 (0.97-3.24) (1.57-3.67) than normal
ECOG 2 9.4 12.5 2.05 0.090 2.17 <0.001 performance <2 90.6
87.5 (0.89-4.71) (1.40-3.35) status Gender Male 42 65 1.62 0.105
2.17 <0.001 Female 68 35 (0.90-2.90) (1.45-3.25) B-symptoms
Present 17.2 21.3 2.05 0.029 2.10 <0.001 Absent 82.8 78.7
(1.08-3.89) (1.37-3.23) Grade.sup.3 1 45 43.4 N/A 0.118 2.55
<0.001 2 34.8 33.3 2.03 (1.63-3.99) (1.04-3.96) 3 20.2 23.3 1.39
(0.65-2.98) Int'l, Scores 63.1 47.5 N/A 0.029 2.28 <0.001
Prognostic 0-1 (1.46-3.57) Index.sup.4 Scores 33.3 45 2.07 2-3
(1.07-4.00) Scores 3.6 7.5 3.73 4-5 (1.18-11.18) .sup.1Due to
rounding, percentages may not total 100 .sup.2Relative risk of
death (RR) based on 2-fold increase in expression .sup.3RR for
grades 2 and 3 calculated with respect to risk of death for grade
1. The p-value is calculated for all grades. .sup.4RR for scores
2-3 and 4-5 calculated with respect to risk of death for scores
0-1. The p-value is calculated for all grades.
[0204] The samples in the validation set were divided into three
groups based on their IPI score, and the relationship between
survival and IPI score was visualized by Kaplan-Meier plot (FIG.
6). Among validation set samples from the low-riak (IPI 0-1) and
intermediate risk (IPI 2-3) IPI groups, the gene-expression-based
survival predictor could stratify patients into groups differing by
more than 5 years with regards to median survival (FIG. 7). The
high-risk IPI group (IPI 4-5) comprised less than 5% of the
samples, and was omitted from this analysis. These results
demonstrate that the gene expression-based model is not merely
acting as a surrogate for clinical variables that are known to
predict survival in FL, but rather it identifies distinct
biological attributes of the tumors that are associated with
survival.
Example 4
Development of a Second FL Survival Predictor Using Gene Expression
Data From Affymetrix U133A and U133B Microarrays
[0205] 191 FL were divided into two equivalent groups: a training
set (95 samples) for developing the survival prediction model, and
a validation set (96 samples) for evaluating the reproducibility of
the model. Gene expression data from Affymetrix U133A and U133B
microarrays was obtained for each of the samples. A Cox
proportional hazards model was used to identify survival predictor
genes whose expression levels were associated with long survival
(good prognosis genes) or short survival (poor prognosis genes) in
the training set. The correlation between expression and survival
for each gene on the microarrays is provided in the final two
columns of Table 1710. The first of these two columns
("FL_Cox_coefficient") provides a Cox coefficient indicating the
extent to which a 2-fold increase in expression of a particular
gene affects mortality. A positive Cox coefficient indicates
increasing mortality with increasing expression of the gene, white
a negative Cox coefficient indicates decreasing mortality with
increasing expression of the gene. The second of these two columns
provides a Cox p-value indicating the estimated probability that
the increase or decrease in survival associated with the gene would
occur by chance if there was no connection between the expression
of the gene and survival.
[0206] A hierarchical clustering algorithm (Eisen 1998) was used to
identify gene expression signatures within the good and poor
prognosis genes according to their expression pattern across all
samples. Eight clusters of coordinated regulated genes were
observed within the good prognosis gene set and six clusters were
observed in the poor prognosis gene sets. The expression level of
every component gene in each of these gene expression signatures
was averaged to create a gene expression signature value. After
averaging, only ten of the gene expression signatures were found
tobe significantly associated with survival in the training set
(p<0.01); To create a multivariate model of survival, different
combinations of these ten gene expression signature averages were
generated and evaluated for their ability to predict survival
within the training set. Among models consisting of two signatures,
an exceptionally strong statistical synergy was noted between one
signature from the good prognosis group and one from the poor
prognosis group. These gene expression signatures were termed
"T-cell" and "macrophage" based on the biological function of
certain genes within each signature. The T-cell gene expression
signature included genes that were typically expressed in T-cells,
while the macrophage gene expression signature included a number of
genes typically expressed in macrophages. Although these two
signatures taken individually were not the best predictors of
survival, the binary model formed by combining the two was more
predictive than any combination of three signatures that did not
contain these two signatures. Using these two signatures as an
anchor, olher signatures were added to the model using a step up
procedure (Drapner 1966). Only one of the remaining eight
signatures, termed the B-cell differentiation signature,
contributed significantly to the model in the training set
(p=0.054). The B-cell differentiation signature included a number
of genes that appear to be involved in B-cell signal transduction.
Table 2364 lists the genes that were used to generate the gene
expression signature values for the T-cell, macrophage, and B-cell
differentiation gene expression signatures.
TABLE-US-00008 TABLE 2364 Unigene ID Build 167 Signature UNIQID
(http://www.ncbi.nlm.nih.gov/UniGene) Gene symbol B-cell
differentiation 1119350 331141 ALDH2 B-cell differentiation 1130922
459987 ANP32B B-cell differentiation 1130923 459987 ANP32B B-cell
differentiation 1099291 130774 C9orf105 B-cell differentiation
1102859 446195 FLJ42418 B-cell differentiation 1120976 245644 GCHFR
B-cell differentiation 1098862 303669 MGC26694 B-cell
differentiation 1111070 202201 B-cell differentiation 1105935
B-cell differentiation 1139017 274424 NANS B-cell differentiation
1108988 3532 NLK B-cell differentiation 1114726 3532 NLK B-cell
differentiation 1097897 266175 PAG B-cell differentiation 1097901
266175 PAG B-cell differentiation 1119813 155342 PRKCD B-cell
differentiation 1123298 20191 SIAH2 B-cell differentiation 1101439
63335 TERF2 B-cell differentiation 1120316 63335 TERF2 B-cell
differentiation 1096035 105794 UGCGL1 T-cell 1134945 81897 KIAA1128
T-cell 1134069 405667 CD8B1 T-cell 1137809 405667 CD8B1 T-cell
1119251 433941 SEPW1 T-cell 1096579 117339 HCST T-cell 1101004 2969
SKI T-cell 1137137 195464 FLNA T-cell 1100871 48353 T-cell 1139461
14770 BIN2 T-cell 1128395 7188 SEMA4C T-cell 1119880 442844 FMOD
T-cell 1130676 194431 KIAA0992 T-cell 1130668 194431 KIAA0992
T-cell 1135968 119000 ACTN1 T-cell 1097329 528675 TEAD1 T-cell
1098548 436639 NFIC T-cell 1123038 119000 ACTN1 T-cell 1128356
415792 C1RL T-cell 1133408 12802 DDEF2 T-cell 1140524 10784 C6orf37
T-cell 1119838 469951 GNAQ T-cell 1097255 380144 T-cell 1098152
377588 KIAA1450 T-cell 1115194 270737 TNFSF13B T-cell 1124760
419149 JAM3 T-cell 1120267 256278 TNFRSF1B T-cell 1137289 36972 CD7
T-cell 1137534 36972 CD7 T-cell 1097307 379754 LOC340061 T-cell
1123613 97087 CD3Z T-cell 1121720 80642 STAT4 T-cell 1120196 173802
TBC1D4 T-cell 1136087 211576 ITK T-cell 1132104 173802 TBC1D4
T-cell 1140391 44865 LEF1 T-cell 1098405 362807 IL7R T-cell 1135743
299558 TNFRSF25 T-cell 1136048 299558 TNFRSF25 T-cell 1123875 428
FLT3LG T-cell 1098893 43577 ATP8B2 T-cell 1097561 19221 C20orf112
T-cell 1122956 113987 LGALS2 T-cell 1121406 TNFSF12 T-cell 1125532
T-cell 1138538 2014 TRD T-cell 1103303 49605 C9orf52 T-cell 1119924
32309 INPP1 Macrophage 1123682 114408 TLR5 Macrophage 1099124
355455 SEPT10 Macrophage 1123401 50130 NDN Macrophage 1134379
150833 C4A Macrophage 1137481 150833 C4A Macrophage 1132220 448805
GPRC5B Macrophage 1119400 181046 DUSP3 Macrophage 1131119 349656
SCARB2 Macrophage 1123566 155935 C3AR1 Macrophage 1138443 77424
FCGR1A Macrophage 1127943 9641 C1QA Macrophage 1119998 8986 C1QB
Macrophage 1132433 14732 ME1 Macrophage 1119260 18069 LGMN
Macrophage 1098278 166017 MITF
The three signatures were used to generate a survival predictor
score using the following equation:
Survival predictor score=[2.053*(macrophage gene expression
signature value)]-[2.344*(T-cell gene expression signature
value)]-[0.729*(B-cell differentiation gene expression signature
value)].
A higher, survival predictor score was associated with worse
outcome. According to a likelihood ratio test adjusted for the
number of variables included, this model was significant in
predicting survival in both the training set
(p=1.8.times.10.sup.-8) and the validation set
(p=2.0.times.10.sup.-5). For the 187 FL samples with available
clinical data, the survival predictor score had a mean of -11.9 and
a standard deviation of 0.9418, with each unit increase in the
predictor score corresponding to a 2.5 fold increase in the
relative risk of death. Data for all 191 samples is shown in Table
2385.
TABLE-US-00009 TABLE 2365 B cell differ- entiation T-cell
Macrophage Survival Sample signature signature signature predictor
ID # Set value value value score FL_1073 Training 9.70 9.14 8.58
-10.89 FL_1074 Training 11.11 9.06 8.52 -11.84 FL_1075 Validation
11.23 8.92 8.75 -11.15 FL_1076 Training 10.02 9.21 8.59 -11.25
FL_1077 Training 9.94 9.77 8.44 -12.82 FL_1078 Training 10.67 9.32
8.21 -12.76 FL_1080 Training 10.62 9.44 8.88 -11.64 FL_1081
Validation 10.38 9.00 8.09 -12.04 FL_1083 Training 10.29 9.77 8.74
-12.47 FL_1085 Validation 9.87 9.24 8.43 -11.55 FL_1086 Validation
10.03 9.50 9.02 -11.06 FL_1087 Training 9.83 9.98 9.37 -11.31
FL_1088 Validation 10.57 9.21 8.29 -12.27 FL_1089 Training 10.30
9.38 8.27 -12.53 FL_1090 Validation 9.74 9.24 8.20 -11.93 FL_1097
Validation 9.57 9.82 8.80 -11.93 FL_1098 Validation 11.08 9.40 8.97
-11.69 FL_1099 Training 10.23 9.70 9.12 -11.46 FL_1102 Validation
9.66 9.46 8.90 -10.93 FL_1104 Training 10.72 9.19 8.20 -12.53
FL_1106 Validation 11.11 9.17 9.57 -9.96 FL_1107 Training 9.70 9.42
9.55 -9.54 FL_1183 Training 9.85 9.25 8.44 -11.54 FL_1184 Training
10.12 9.57 8.86 -11.63 FL_1185 Validation 10.75 9.21 9.13 -10.68
FL_1186 Training 9.76 8.88 8.83 -9.80 FL_1416 Validation 9.94 9.45
8.59 -11.77 FL_1417 Training 10.12 8.53 8.43 -10.08 FL_1418
Validation 9.35 8.86 8.27 -10.59 FL_1419 Training 10.20 9.76 8.53
-12.81 FL_1422 Training 10.22 9.48 8.40 -12.43 FL_1425 Validation
9.61 8.89 8.58 -10.23 FL_1426 Training 10.80 9.06 8.13 -12.41
FL_1427 Training 10.27 8.56 8.13 -10.87 FL_1428 Validation 10.76
9.25 8.38 -12.32 FL_1432 Training 10.51 9.17 9.04 -10.59 FL_1436
Training 9.69 9.40 8.61 -11.42 FL_1440 Training 9.82 9.04 8.21
-11.50 FL_1445 Training 9.24 8.69 8.62 -9.41 FL_1450 Validation
9.70 9.88 10.37 -8.93 FL_1472 Validation 10.78 8.96 8.51 -11.40
FL_1473 Training 9.99 9.70 8.41 -12.75 FL_1474 Validation 10.21
9.27 9.05 -10.59 FL_1476 Validation 9.82 9.44 8.78 -11.27 FL_1477
Training 9.32 9.61 9.03 -10.78 FL_1478 Training 10.19 9.60 8.81
-11.83 FL_1479 Training 10.69 8.78 9.09 -9.71 FL_1480 Training
10.10 9.42 8.70 -11.57 FL_1579 Training 10.15 8.82 8.24 -11.15
FL_1580 Training 10.31 9.59 8.50 -12.54 FL_1581 Training 9.91 8.96
9.05 -9.66 FL_1582 Validation 9.73 8.31 8.06 -10.03 FL_1583
Training 10.95 9.45 8.86 -11.95 FL_1584 Training 9.98 9.38 8.46
-11.89 FL_1585 Validation 10.53 8.88 8.46 -11.11 FL_1586 Validation
10.00 9.30 8.42 -11.81 FL_1588 Training 9.59 9.41 8.94 -10.68
FL_1589 Training 10.29 9.68 8.73 -12.27 FL_1591 Training 10.44 9.45
8.56 -12.18 FL_1594 Validation 10.01 9.25 8.56 -11.41 FL_1595
Training 9.61 9.75 9.65 -10.07 FL_1598 Validation 11.18 8.80 8.31
-11.71 FL_1599 Validation 10.55 9.48 8.60 -12.24 FL_1603 Training
9.40 9.60 9.77 -9.31 FL_1604 Training 9.92 9.21 8.90 -10.54 FL_1606
Validation 9.87 9.45 9.17 -10.52 FL_1607 Validation 9.76 9.37 8.50
-11.63 FL_1608 Validation 9.92 8.90 8.39 -10.85 FL_1610 Validation
10.02 9.38 9.74 -9.30 FL_1611 Validation 10.18 9.41 8.69 -11.64
FL_1616 Training 9.62 9.33 8.85 -10.71 FL_1617 Validation 9.90 8.95
8.39 -10.98 FL_1619 Validation 9.98 9.37 8.47 -11.85 FL_1620
Validation 9.43 8.95 8.12 -11.19 FL_1622 Training 9.84 9.15 8.31
-11.56 FL_1623 Training 9.95 9.61 8.97 -11.37 FL_1624 Validation
10.55 9.06 8.43 -11.61 FL_1625 Validation 10.00 8.89 8.23 -11.22
FL_1626 Validation 11.05 8.62 8.10 -11.62 FL_1628 Validation 10.08
9.81 8.66 -12.57 FL_1637 Validation 9.77 9.95 9.59 -10.76 FL_1638
Validation 10.25 9.20 9.07 -10.41 FL_1639 Training 10.29 9.52 8.99
-11.35 FL_1643 Training 9.80 9.72 9.00 -11.46 FL_1644 Validation
9.51 9.46 8.61 -11.43 FL_1645 Training 9.39 9.46 8.70 -11.15
FL_1646 Training 9.90 9.25 8.52 -11.42 FL_1647 Training 9.51 9.12
8.95 -9.92 FL_1648 Training 10.02 9.18 7.86 -12.67 FL_1652 Training
9.62 9.39 9.19 -10.16 FL_1654 Validation 10.32 8.59 8.10 -11.02
FL_1655 Training 10.12 9.53 8.75 -11.74 FL_1656 Validation 10.54
9.08 8.55 -11.42 FL_1657 Training 10.53 9.53 8.55 -12.46 FL_1660
Training 10.24 8.75 8.27 -10.99 FL_1661 Validation 10.08 9.85 9.00
-11.97 FL_1662 Validation 9.85 9.56 9.49 -10.11 FL_1664 Validation
10.16 9.35 8.48 -11.92 FL_1669 Training 9.48 8.76 8.28 -10.45
FL_1670 Training 9.76 9.66 9.66 -9.92 FL_1675 Training 10.57 9.28
8.41 -12.18 FL_1681 Validation 10.48 9.52 8.66 -12.19 FL_1683
Validation 9.88 9.92 9.07 -11.83 FL_1684 Training 9.64 9.53 8.85
-11.20 FL_1716 Validation 9.90 8.91 8.22 -11.23 FL_1717 Validation
9.87 9.34 8.95 -10.71 FL_1718 Training 10.00 9.21 7.98 -12.49
FL_1719 Validation 9.87 9.06 8.42 -11.14 FL_1720 Training 10.70
8.77 8.92 -10.05 FL_1729 Training 10.50 9.23 8.65 -11.53 FL_1732
Validation 9.91 7.68 8.54 -7.69 FL_1761 Validation 9.81 9.22 8.39
-11.54 FL_1764 Training 9.81 9.24 8.77 -10.80 FL_1768 Training
10.12 9.36 8.50 -11.86 FL_1771 Training 9.92 9.12 8.68 -10.79
FL_1772 Validation 9.72 9.42 8.43 -11.87 FL_1788 Training 9.65 9.05
9.12 -9.51 FL_1790 Training 9.58 9.83 9.48 -10.56 FL_1792
Validation 9.79 9.29 8.67 -11.11 FL_1795 Training 9.58 10.18 9.33
-11.69 FL_1797 Validation 9.93 9.26 8.79 -10.90 FL_1799 Training
10.49 9.28 8.64 -11.65 FL_1810 Validation 10.06 8.55 8.21 -10.52
FL_1811 Validation 9.84 9.37 8.08 -12.56 FL_1825 Training 10.49
9.44 9.03 -11.24 FL_1827 Training 10.06 9.76 8.84 -12.08 FL_1828
Validation 10.55 8.93 7.67 -12.87 FL_1829 Validation 9.85 9.58 8.65
-11.87 FL_1830 Validation 10.80 8.99 8.67 -11.15 FL_1833 Training
10.41 9.83 8.82 -12.52 FL_1834 Validation 10.81 9.25 8.63 -11.85
FL_1835 Validation 9.36 9.25 8.91 -10.21 FL_1836 Validation 10.58
9.58 8.61 -12.50 FL_1837 Validation 10.22 9.47 8.76 -11.68 FL_1838
Validation 10.51 9.89 9.19 -11.98 FL_1839 Training 10.79 8.54 8.19
-11.09 FL_1841 Training 10.32 9.31 9.18 -10.48 FL_1842 Validation
10.36 9.69 8.92 -11.95 FL_1844 Validation 10.92 9.43 8.49 -12.65
FL_1845 Training 9.87 9.87 9.06 -11.73 FL_1846 Validation 9.66 9.81
9.93 -9.63 FL_1848 Training 9.82 9.74 8.70 -12.14 FL_1851 Training
9.89 9.47 9.03 -10.87 FL_1853 Validation 9.96 9.28 8.54 -11.49
FL_1854 Validation 9.97 9.29 8.73 -11.12 FL_1855 Validation 9.95
9.33 8.42 -11.85 FL_1857 Validation 10.35 9.81 9.28 -11.50 FL_1861
Validation 9.73 9.46 8.43 -11.96 FL_1862 Validation 10.42 8.94 8.22
-11.69 FL_1863 Validation 10.79 9.29 8.82 -11.54 FL_1864 Training
9.67 9.97 9.07 -11.80 FL_1866 Training 10.19 9.88 8.89 -12.33
FL_1870 Validation 9.78 10.07 9.30 -11.63 FL_1873 Training 10.09
9.41 8.77 -11.40 FL_1874 Validation 10.05 9.33 8.69 -11.37 FL_1876
Validation 10.15 9.59 8.67 -12.08 FL_1879 Training 9.73 9.21 8.58
-11.06 FL_1880 Validation 10.02 8.79 8.35 -10.77 FL_1882 Training
9.59 9.44 8.80 -11.05 FL_1884 Validation 9.76 9.51 9.26 -10.38
FL_1885 Validation 10.48 9.66 8.75 -12.32 FL_1887 Training 9.98
9.42 8.47 -11.96 FL_1888 Training 9.73 9.83 8.99 -11.67 FL_1890
Training 10.06 9.33 8.98 -10.76 FL_1894 Training 9.85 8.99 8.75
-10.29 FL_1896 Training 10.21 9.80 8.51 -12.94 FL_1897 Training
10.67 8.99 8.26 -11.90 FL_1898 Training 9.59 8.77 8.21 -10.68
FL_1900 Validation 10.12 9.10 8.10 -12.08 FL_1903 Validation 11.08
8.99 8.39 -11.93 FL_1904 Validation 10.20 9.16 8.30 -11.87 FL_1905
Validation 9.73 9.21 8.22 -11.80 FL_1906 Training 9.95 8.15 8.44
-9.01 FL_1907 Validation 10.12 7.95 7.99 -9.62 FL_1910 Training
11.03 9.38 8.74 -12.10 FL_1912 Validation 9.83 9.38 9.36 -9.95
FL_1913 Training 9.81 9.75 8.43 -12.69 FL_1916 Validation 9.83 9.18
8.40 -11.43 FL_1918 Validation 9.86 9.52 8.79 -11.45 FL_1919
Training 9.87 9.53 8.79 -11.48 FL_735 Validation 10.48 8.73 8.23
-11.20 FL_738 Validation 11.05 9.10 8.75 -11.43 FL_739 Training
9.66 9.25 8.74 -10.78 FL_878 Validation 10.61 8.92 8.65 -10.89
FL_879 Training 9.92 8.94 8.78 -10.14 FL_886 Validation 10.16 9.41
8.63 -11.73 FL_888 Validation 9.35 8.76 8.38 -10.15 FL_1627
Training 9.82 9.48 8.49 -11.94 FL_1429 Training 10.06 8.70 8.14
-11.01 FL_1850 Validation 9.58 9.73 8.70 -11.93 FL_1735 Validation
9.60 7.46 8.42 -7.19
[0207] In order to visualize the predictive power of the model, the
FL samples were ranked according to their survival predictor scores
and divided into four quartiles. Kaplan-Meier plots of overall
survival showed clear differences in survival rate in the
validation set (FIG. 8). The median survival for each of the four
quartiles is set forth in Table 2366.
TABLE-US-00010 TABLE 2366 Quartile Median survival (yrs.) 5-year
survival 10-year survival 1 NR 94% 79% 2 11.6 82% 62% 3 8.8 69% 39%
4 3.9 38% 22%
Example 5
Development of a Third FL Survival Predictor Using Gene Expression
Data From the Lymph Dx Microarray
[0208] 191 FL samples were divided into two equivalent groups: a
training set for developing the survival prediction model, and a
validation set for evaluating the reproducibility of the model.
Gene expression data from the Lymph Dx microarray was obtained for
those genes listed in Table 2364, above. This gene expression data
was used to calculate gene expression signature values for the
macrophage, T-cell, and B-cell differentiation gene expression
signatures, and these signature values were used to generate a
survival predictor score using the following equation:
Survival predictor score=[1.51*(macrophage gene expression
signature value)]-[2.11*(T-cell gene expression signature
value)]-[0.505*(B-cell differentiation gene expression signature
value)].
A higher survival predictor score was associated with worse
outcome. For the 187 FL samples with available clinical data, the
survival predictor score had a mean of -10.1 and a standard
deviation 0.69, with each unit increase in the predictor score
corresponding to a 2.7 fold increase in the relative risk of death.
Data for all 191 samples is shown in Table 2367.
TABLE-US-00011 TABLE 2367 B cell differ- entiation T-cell
Macrophage Survival Sample signature signature signature predictor
ID # Set value value value score FL_1073 Training 8.26 8.17 7.36
-10.30 FL_1074 Training 9.53 8.12 7.56 -10.53 FL_1075 Validation
9.81 8.00 7.99 -9.77 FL_1076 Training 8.46 8.10 7.62 -9.86 FL_1077
Training 8.45 8.66 7.32 -11.49 FL_1078 Training 9.23 8.32 7.32
-11.18 FL_1080 Training 9.18 8.37 7.86 -10.42 FL_1081 Validation
8.96 8.01 6.94 -10.96 FL_1083 Training 8.72 8.66 7.89 -10.75
FL_1085 Validation 8.34 8.17 7.54 -10.07 FL_1086 Validation 8.50
8.35 7.94 -9.94 FL_1087 Training 8.02 8.88 8.48 -10.00 FL_1088
Validation 9.10 8.15 7.38 -10.65 FL_1089 Training 8.76 8.31 7.35
-10.86 FL_1090 Validation 8.18 8.23 7.43 -10.28 FL_1097 Validation
8.07 8.81 7.90 -10.73 FL_1098 Validation 9.53 8.30 8.09 -10.11
FL_1099 Training 8.44 8.56 8.26 -9.86 FL_1102 Validation 7.92 8.43
7.94 -9.80 FL_1104 Training 9.17 8.07 7.21 -10.78 FL_1106
Validation 9.71 8.15 8.77 -8.85 FL_1107 Training 8.16 8.44 8.60
-8.95 FL_1183 Training 8.49 8.15 7.23 -10.56 FL_1184 Training 8.81
8.49 7.91 -10.43 FL_1185 Validation 9.31 8.19 8.06 -9.80 FL_1186
Training 8.43 7.87 7.83 -9.04 FL_1416 Validation 8.42 8.34 7.63
-10.34 FL_1417 Training 8.65 7.51 7.05 -9.58 FL_1418 Validation
7.96 7.82 7.22 -9.62 FL_1419 Training 8.80 8.71 7.55 -11.43 FL_1422
Training 8.63 8.35 7.39 -10.83 FL_1425 Validation 8.21 7.92 7.62
-9.36 FL_1426 Training 9.39 8.09 7.15 -11.01 FL_1427 Training 8.66
7.51 7.00 -9.65 FL_1428 Validation 9.33 8.18 7.39 -10.81 FL_1432
Training 8.98 8.17 7.93 -9.81 FL_1436 Training 8.04 8.17 7.35
-10.20 FL_1440 Training 8.29 7.82 7.15 -9.89 FL_1445 Training 8.04
7.78 7.63 -8.94 FL_1450 Validation 8.25 8.81 9.52 -8.39 FL_1472
Validation 9.29 7.88 7.33 -10.26 FL_1473 Training 8.49 8.57 7.52
-11.03 FL_1474 Validation 8.59 8.09 8.53 -8.54 FL_1476 Validation
8.25 8.39 7.71 -10.23 FL_1477 Training 7.94 8.57 7.88 -10.21
FL_1478 Training 8.57 8.40 7.88 -10.16 FL_1479 Training 9.15 7.83
7.87 -9.27 FL_1480 Training 8.25 8.38 7.44 -10.63 FL_1579 Training
8.70 7.73 7.43 -9.48 FL_1580 Training 8.86 8.46 7.64 -10.79 FL_1581
Training 8.41 7.89 8.08 -8.69 FL_1582 Validation 8.20 7.42 6.99
-9.24 FL_1583 Training 9.34 8.34 7.94 -10.32 FL_1584 Training 8.50
8.33 7.75 -10.17 FL_1585 Validation 9.08 7.98 7.72 -9.72 FL_1586
Validation 8.52 8.25 7.36 -10.61 FL_1588 Training 7.97 8.35 7.73
-9.98 FL_1589 Training 8.85 8.48 7.76 -10.66 FL_1591 Training 8.92
8.36 7.77 -10.42 FL_1594 Validation 8.54 8.22 7.74 -9.96 FL_1595
Training 8.05 8.82 8.68 -9.57 FL_1598 Validation 9.74 7.81 6.97
-10.88 FL_1599 Validation 9.13 8.42 7.69 -10.77 FL_1603 Training
7.97 8.66 8.90 -8.86 FL_1604 Training 8.47 8.14 7.75 -9.75 FL_1606
Validation 8.34 8.32 8.11 -9.51 FL_1607 Validation 8.33 8.30 7.39
-10.57 FL_1608 Validation 8.35 7.88 6.98 -10.31 FL_1610 Validation
8.48 8.35 8.86 -8.52 FL_1611 Validation 8.54 8.33 7.64 -10.37
FL_1616 Training 8.03 8.39 7.67 -10.18 FL_1617 Validation 8.30 7.85
7.52 -9.40 FL_1619 Validation 8.53 8.31 7.64 -10.32 FL_1620
Validation 8.09 7.99 7.17 -10.11 FL_1622 Training 8.14 8.10 7.36
-10.09 FL_1623 Training 8.45 8.52 8.15 -9.93 FL_1624 Validation
9.13 8.12 7.46 -10.49 FL_1625 Validation 8.53 7.94 7.17 -10.23
FL_1626 Validation 9.63 7.67 7.17 -10.22 FL_1628 Validation 8.63
8.76 7.95 -10.86 FL_1637 Validation 8.07 8.81 8.79 -9.38 FL_1638
Validation 8.52 8.18 8.19 -9.18 FL_1639 Training 8.70 8.33 7.89
-10.06 FL_1643 Training 8.26 8.62 8.01 -10.26 FL_1644 Validation
8.28 8.33 7.77 -10.02 FL_1645 Training 7.84 8.32 7.68 -9.91 FL_1646
Training 8.40 8.26 7.71 -10.01 FL_1647 Training 8.10 8.04 7.92
-9.10 FL_1648 Training 8.33 8.08 6.87 -10.90 FL_1652 Training 8.15
8.33 8.37 -9.07 FL_1654 Validation 8.67 7.62 7.03 -9.85 FL_1655
Training 8.53 8.41 7.75 -10.36 FL_1656 Validation 9.09 8.09 7.62
-10.16 FL_1657 Training 8.95 8.44 7.58 -10.89 FL_1660 Training 8.82
7.79 7.26 -9.93 FL_1661 Validation 8.56 8.79 8.17 -10.53 FL_1662
Validation 8.30 8.47 8.69 -8.93 FL_1664 Validation 8.62 8.23 7.56
-10.31 FL_1669 Training 7.89 7.67 7.39 -9.02 FL_1670 Training 8.01
8.54 8.64 -9.03 FL_1675 Training 9.00 8.21 7.36 -10.76 FL_1681
Validation 8.83 8.39 7.59 -10.72 FL_1683 Validation 8.14 8.85 7.97
-10.74 FL_1684 Training 7.99 8.42 7.84 -9.97 FL_1716 Validation
8.28 7.90 7.26 -9.88 FL_1717 Validation 8.27 8.21 7.89 -9.60
FL_1718 Training 8.50 8.17 7.15 -10.75 FL_1719 Validation 8.35 8.02
7.21 -10.26 FL_1720 Training 9.03 7.65 8.01 -8.61 FL_1729 Training
8.97 8.27 7.69 -10.37 FL_1732 Validation 8.49 6.82 7.71 -7.02
FL_1761 Validation 8.36 8.19 7.29 -10.49 FL_1764 Training 8.52 8.24
7.94 -9.69 FL_1768 Training 8.70 8.25 7.63 -10.28 FL_1771 Training
8.55 8.19 7.65 -10.04 FL_1772 Validation 8.30 8.38 7.41 -10.71
FL_1788 Training 8.14 8.06 8.11 -8.87 FL_1790 Training 7.95 8.69
8.36 -9.74 FL_1792 Validation 8.16 8.20 7.64 -9.88 FL_1795 Training
7.94 9.08 8.37 -10.54 FL_1797 Validation 8.17 8.21 7.87 -9.57
FL_1799 Training 9.02 8.21 7.77 -10.14 FL_1810 Validation 8.43 7.52
7.06 -9.47 FL_1811 Validation 8.33 8.24 7.07 -10.93 FL_1825
Training 8.90 8.39 7.97 -10.18 FL_1827 Training 8.47 8.77 7.96
-10.76 FL_1828 Validation 9.13 7.87 6.76 -11.01 FL_1829 Validation
8.34 8.51 7.59 -10.71 FL_1830 Validation 9.26 8.04 7.62 -10.13
FL_1833 Training 8.82 8.86 7.88 -11.26 FL_1834 Validation 9.25 8.17
7.62 -10.39 FL_1835 Validation 7.71 8.16 8.01 -9.02 FL_1836
Validation 9.06 8.52 7.59 -11.09 FL_1837 Validation 8.57 8.33 7.37
-10.79 FL_1838 Validation 8.78 8.72 8.04 -10.69 FL_1839 Training
9.27 7.36 7.37 -9.08 FL_1841 Training 8.66 8.35 8.17 -9.64 FL_1842
Validation 8.62 8.50 8.02 -10.19 FL_1844 Validation 9.37 8.40 7.47
-11.18 FL_1845 Training 8.33 8.84 8.30 -10.32 FL_1846 Validation
8.11 8.75 9.06 -8.89 FL_1848 Training 8.19 8.60 7.91 -10.33 FL_1851
Training 8.37 8.50 8.15 -9.84 FL_1853 Validation 8.37 8.14 7.43
-10.19 FL_1854 Validation 8.50 8.29 7.96 -9.78 FL_1855 Validation
8.63 8.34 7.54 -10.58 FL_1857 Validation 8.73 8.82 8.45 -10.26
FL_1861 Validation 8.21 8.50 7.50 -10.77 FL_1862 Validation 8.98
7.96 7.31 -10.28 FL_1863 Validation 9.30 8.22 7.86 -10.18 FL_1864
Training 8.13 8.93 8.27 -10.46 FL_1866 Training 8.62 8.78 7.91
-10.93 FL_1870 Validation 8.18 8.97 8.52 -10.18 FL_1873 Training
8.55 8.30 8.00 -9.74 FL_1874 Validation 8.43 8.20 7.59 -10.10
FL_1876 Validation 8.48 8.52 7.70 -10.64 FL_1879 Training 8.29 8.21
7.66 -9.94 FL_1880 Validation 8.56 7.76 7.34 -9.61 FL_1882 Training
8.02 8.40 7.71 -10.14 FL_1884 Validation 8.14 8.46 8.42 -9.24
FL_1885 Validation 8.88 8.57 7.78 -10.81 FL_1887 Training 8.38 8.39
7.38 -10.78 FL_1888 Training 8.14 8.74 8.07 -10.37 FL_1890 Training
8.45 8.24 8.11 -9.41 FL_1894 Training 8.38 7.97 7.82 -9.25 FL_1896
Training 8.63 8.71 7.52 -11.37 FL_1897 Training 9.01 7.91 6.93
-10.78 FL_1898 Training 8.08 7.75 7.09 -9.74 FL_1900 Validation
8.61 7.94 6.84 -10.77 FL_1903 Validation 9.63 7.96 7.30 -10.64
FL_1904 Validation 8.79 8.14 7.15 -10.82 FL_1905 Validation 8.22
8.24 7.36 -10.43 FL_1906 Training 8.40 7.40 7.24 -8.93 FL_1907
Validation 8.61 7.11 6.59 -9.40 FL_1910 Training 9.47 8.28 7.63
-10.73 FL_1912 Validation 8.32 8.45 8.52 -9.18 FL_1913 Training
8.24 8.60 7.23 -11.41 FL_1916 Validation 8.31 8.04 7.27 -10.19
FL_1918 Validation 8.30 8.49 7.78 -10.37 FL_1919 Training 8.05 8.42
8.00 -9.75 FL_735 Validation 9.03 7.83 7.41 -9.88 FL_738 Validation
9.54 8.07 7.65 -10.30 FL_739 Training 8.14 8.09 7.69 -9.57 FL_878
Validation 9.17 7.91 7.70 -9.69 FL_879 Training 8.37 7.96 7.67
-9.45 FL_886 Validation 8.59 8.38 7.67 -10.44 FL_888 Validation
7.85 7.71 7.07 -9.56 FL_1627 Training 8.26 8.17 7.36 -10.30 FL_1429
Training 9.53 8.12 7.56 -10.53 FL_1850 Validation 9.81 8.00 7.99
-9.77 FL_1735 Validation 8.46 8.10 7.62 -9.86
[0209] In order to visualize the predictive power of the model, the
FL samples were ranked according to their survival predictor scores
and divided into four quartiles. Kaplan-Meier plots of overall
survival showed clear differences in survival rate in the
validation set (FIG. 9).
Example 6
Development of a First DLBCL Survival Predictor Using Gene
Expression Data From Affymetrix U133A and U133B Microarrays
[0210] Gene expression data from Affymetrix U133A and U133B
microarrays was obtained for 231 DLBCL samples. The follow-up time
and status at follow-up for each of the subjects from whom these
samples were acquired is listed in Table 2368. Table 2368 also
indicates which samples were used in creating the survival
predictor.
TABLE-US-00012 TABLE 2368 Length of Status at Used in creating
Sample ID # follow-up (years) follow-up survival predictor?
ABC_1000 0.69 Dead Yes ABC_1002 0.28 Dead Yes ABC_1023 5.57 Dead
Yes ABC_1027 0.25 Dead Yes ABC_1031 6.64 Dead Yes ABC_1034 2.31
Dead Yes ABC_1038 0.71 Dead Yes ABC_1043 2.31 Dead Yes ABC_1045
2.26 Dead Yes ABC_1055 7.81 Alive Yes ABC_1057 2.13 Dead Yes
ABC_1059 2.00 Dead Yes ABC_1061 1.04 Dead Yes ABC_1946 0.68 Dead No
ABC_1994 1.21 Dead No ABC_2001 1.32 Dead No ABC_304 1.31 Dead Yes
ABC_305 0.82 Alive Yes ABC_309 2.80 Alive Yes ABC_413 0.60 Dead Yes
ABC_428 11.38 Alive Yes ABC_432 0.38 Dead Yes ABC_446 2.82 Dead Yes
ABC_462 7.49 Dead Yes ABC_477 1.70 Dead Yes ABC_481 10.75 Alive Yes
ABC_482 7.72 Alive Yes ABC_538 0.34 Dead Yes ABC_541 4.11 Alive Yes
ABC_544 1.31 Dead Yes ABC_547 0.05 Dead Yes ABC_577 1.65 Alive Yes
ABC_616 0.99 Dead Yes ABC_626 2.49 Dead Yes ABC_633 2.02 Alive Yes
ABC_642 0.34 Dead Yes ABC_644 0.31 Dead Yes ABC_645 6.08 Dead Yes
ABC_646 2.59 Dead Yes ABC_651 2.34 Alive Yes ABC_652 0.01 Dead Yes
ABC_660 0.20 Dead Yes ABC_663 0.62 Dead Yes ABC_668 6.44 Alive Yes
ABC_676 1.00 Dead Yes ABC_678 0.06 Dead Yes ABC_687 0.94 Dead Yes
ABC_689 2.54 Dead Yes ABC_692 10.53 Alive Yes ABC_694 4.83 Alive
Yes ABC_700 5.40 Dead Yes ABC_702 4.13 Dead Yes ABC_704 9.67 Alive
Yes ABC_709 0.47 Dead Yes ABC_712 3.26 Dead Yes ABC_714 2.45 Dead
Yes ABC_717 0.42 Dead Yes ABC_725 0.96 Dead Yes ABC_726 7.62 Alive
Yes ABC_730 1.03 Dead Yes ABC_753 0.04 Dead Yes ABC_756 7.21 Alive
Yes ABC_771 6.80 Dead Yes ABC_779 0.35 Dead Yes ABC_800 0.33 Dead
Yes ABC_807 0.31 Dead Yes ABC_809 0.51 Dead Yes ABC_816 1.86 Dead
Yes ABC_820 1.59 Dead Yes ABC_823 0.16 Dead Yes ABC_835 1.22 Dead
Yes ABC_839 0.29 Dead Yes ABC_841 10.14 Alive Yes ABC_858 3.58 Dead
Yes ABC_872 5.00 Alive Yes ABC_875 8.45 Alive Yes ABC_912 16.79
Alive Yes ABC_996 0.21 Dead Yes GCB_1005 5.77 Alive Yes GCB_1008
6.46 Alive Yes GCB_1009 9.68 Alive Yes GCB_1021 14.59 Alive Yes
GCB_1025 2.86 Dead Yes GCB_1026 6.94 Dead Yes GCB_1037 0.23 Dead
Yes GCB_1039 2.05 Dead Yes GCB_1049 1.33 Dead Yes GCB_1051 0.12
Dead Yes GCB_1058 0.42 Dead Yes GCB_1060 6.45 Alive Yes GCB_1990
0.06 Dead No GCB_1991 1.01 Dead No GCB_2017 0.08 Dead No GCB_2018
0.17 Dead No GCB_2095 0.97 Alive No GCB_412 12.12 Alive Yes GCB_415
5.38 Dead Yes GCB_421 1.24 Dead Yes GCB_424 10.62 Dead Yes GCB_433
0.76 Dead Yes GCB_434 10.53 Alive Yes GCB_438 8.15 Alive Yes
GCB_459 9.65 Alive Yes GCB_470 11.17 Alive Yes GCB_479 7.24 Alive
Yes GCB_492 11.29 Alive Yes GCB_517 3.03 Dead Yes GCB_523 8.36
Alive Yes GCB_524 5.88 Alive Yes GCB_529 1.06 Dead Yes GCB_533 0.71
Dead Yes GCB_537 4.99 Dead Yes GCB_543 3.47 Alive Yes GCB_545 1.10
Dead Yes GCB_549 2.68 Dead Yes GCB_550 21.78 Alive Yes GCB_553 0.82
Dead Yes GCB_565 9.11 Dead Yes GCB_572 14.24 Alive Yes GCB_617 5.88
Alive Yes GCB_618 5.65 Alive Yes GCB_619 8.76 Alive Yes GCB_623
2.43 Alive Yes GCB_627 1.27 Dead Yes GCB_654 7.37 Alive Yes GCB_661
0.56 Alive Yes GCB_669 7.11 Alive Yes GCB_672 6.78 Alive Yes
GCB_674 7.22 Alive Yes GCB_675 6.02 Alive Yes GCB_681 9.70 Alive
Yes GCB_688 0.33 Dead Yes GCB_695 0.15 Dead Yes GCB_698 3.88 Alive
Yes GCB_701 3.90 Alive Yes GCB_710 1.08 Dead Yes GCB_711 3.93 Dead
Yes GCB_722 3.32 Alive Yes GCB_724 1.40 Dead Yes GCB_731 10.18
Alive Yes GCB_742 4.09 Alive Yes GCB_744 8.86 Alive Yes GCB_745
1.33 Dead Yes GCB_747 15.41 Alive Yes GCB_749 10.40 Alive Yes
GCB_758 1.10 Dead Yes GCB_772 2.48 Alive Yes GCB_777 4.27 Dead Yes
GCB_792 5.53 Alive Yes GCB_795 3.43 Alive Yes GCB_797 6.87 Dead Yes
GCB_803 1.45 Dead Yes GCB_810 11.72 Alive Yes GCB_817 2.76 Dead Yes
GCB_818 0.10 Dead Yes GCB_819 0.72 Dead Yes GCB_821 9.47 Alive Yes
GCB_832 4.01 Alive Yes GCB_836 4.29 Alive Yes GCB_840 3.40 Alive
Yes GCB_847 4.16 Alive Yes GCB_860 3.03 Dead Yes GCB_871 0.41 Dead
Yes GCB_874 0.12 Dead Yes GCB_995 6.65 Alive Yes PMBL_1006 7.12
Alive Yes PMBL_1024 19.83 Alive Yes PMBL_1048 7.70 Alive Yes
PMBL_1053 1.04 Dead Yes PMBL_1920 1.97 Alive No PMBL_1921 4.16
Alive No PMBL_1923 1.60 Alive No PMBL_1924 6.11 Alive No PMBL_1935
12.42 Alive No PMBL_1941 0.71 Alive No PMBL_1942 0.88 Alive No
PMBL_1943 8.96 Alive No PMBL_1945 0.84 Dead No PMBL_1948 7.96 Alive
No PMBL_1949 4.28 Alive No PMBL_1989 1.33 Dead No PMBL_1992 1.00
Dead No PMBL_1993 1.33 Dead No PMBL_2002 6.62 Alive No PMBL_2019
0.99 Dead No PMBL_2020 2.08 Alive No PMBL_2092 1.27 Alive No
PMBL_484 1.40 Dead Yes PMBL_546 0.78 Dead Yes PMBL_570 14.40 Alive
Yes PMBL_621 8.14 Alive Yes PMBL_638 0.70 Dead Yes PMBL_691 0.32
Dead Yes PMBL_791 1.33 Dead Yes PMBL_824 12.24 Alive Yes PMBL_906
16.80 Alive Yes PMBL_994 4.79 Alive Yes PMBL_998 9.11 Alive Yes
UC_DLBCL_1001 0.33 Dead Yes UC_DLBCL_1004 6.72 Alive Yes
UC_DLBCL_1007 2.26 Dead Yes UC_DLBCL_1018 0.03 Dead Yes
UC_DLBCL_1041 3.13 Dead Yes UC_DLBCL_1054 12.34 Alive Yes
UC_DLBCL_306 2.69 Alive Yes UC_DLBCL_310 0.97 Alive Yes
UC_DLBCL_449 9.16 Alive Yes UC_DLBCL_452 9.17 Alive Yes
UC_DLBCL_458 1.18 Dead Yes UC_DLBCL_460 9.02 Alive Yes UC_DLBCL_491
4.47 Dead Yes UC_DLBCL_528 1.64 Alive Yes UC_DLBCL_615 4.94 Alive
Yes UC_DLBCL_625 5.24 Alive Yes UC_DLBCL_664 0.62 Dead Yes
UC_DLBCL_671 3.35 Alive Yes UC_DLBCL_682 0.11 Dead Yes UC_DLBCL_683
7.42 Alive Yes UC_DLBCL_684 1.92 Dead Yes UC_DLBCL_748 1.01 Dead
Yes UC_DLBCL_751 9.99 Alive Yes UC_DLBCL_808 0.37 Dead Yes
UC_DLBCL_831 11.02 Dead Yes UC_DLBCL_834 1.64 Dead Yes UC_DLBCL_838
0.00 Dead Yes UC_DLBCL_851 0.05 Dead Yes UC_DLBCL_854 1.51 Dead Yes
UC_DLBCL_855 1.67 Alive Yes UC_DLBCL_856 0.60 Dead Yes
[0211] The correlation between expression of each gene represented
on the microarrays and survival was estimated using a Cox
proportional hazards model. The results of this survival analysis
are provided in the final two columns of Table 1723. The first of
these two columns ("DLBCL_Cox_coefficient") provides a Cox
coefficient indicating the extent to which a 2-fold increase in
expression of a particular gene affects mortality. A positive Cox
coefficient indicates increasing mortality with increasing
expression of the gene, while a negative Cox coefficient indicates
decreasing mortality with increasing expression of the gene. The
second of these two columns ("DLBCL_Cox_P_value") provides a Cdx
p-value indicating the estimated probability that the increase or
decrease in survival associated with the gene would occur by chance
if there was no connection between the expression of the gene and
survival.
[0212] Genes that were significantly correlated with survival
(p<0.001) were grouped into gene expression signatures using a
hierarchical clustering algorithm. The expression level of every
component gene in each of these gene expression signatures was
averaged for each sample to create a gene expression signature
value. A step-up procedure (Drapner 1966) was applied to determine
the optimal number of gene signatures to use in the survival
predictor model. First, the gene expression signature that was most
significantly associated with survival was included in the model.
Next, the gene expression signature with the second highest
association with survival was added to the model to form a
two-component model. This procedure was repeated until there was no
gene expression signature to add to the model with a p-value of
<0.05.
[0213] The final prediction model incorporated gene expression
signature values from three gene expression signatures. The first
gene expression signature added to the model was termed "ABC DLBCL
high," because it included genes that were more highly expressed in
ABC than in GCB (Rosenwald 2002). The second gene expression
signature added to the model was termed "lymph node," because it
reflected the response of non-tumor cells in the lymph node to the
malignant lymphoma cells. The final gene expression signature added
to the model was termed "MHC class II," because it included all of
the genes encoding the MHC class II alpha and beta chains. Table
2369 shows the genes that were averaged to form each of these
signatures.
TABLE-US-00013 TABLE 2369 Signature UNIQID Gene symbol Survival
p-value ABC DLBCL high 1134271 POU5F1 3.09E-05 ABC DLBCL high
1121564 DRIL1 4.06E-05 ABC DLBCL high 1119889 PDCD4 7.28E-05 ABC
DLBCL high 1133300 CTH 1.23E-04 ABC DLBCL high 1106030 MGC:50789
1.70E-04 ABC DLBCL high 1139301 FLJ20150 4.49E-04 ABC DLBCL high
1122131 CHST7 5.18E-04 ABC DLBCL high 1114824 LIMD1 5.20E-04 ABC
DLBCL high 1100161 LOC142678 6.24E-04 ABC DLBCL high 1120129 TLE1
6.95E-04 Lymph node 1097126 TEM8 5.14E-09 Lymph node 1120880 LTBP2
9.80E-07 Lymph node 1098898 FLJ31056 1.09E-06 Lymph node 1123376
RARRES2 1.68E-06 Lymph node 1128945 SLC12A8 2.90E-06 Lymph node
1130994 DPYSL3 3.37E-06 Lymph node 1124429 SULF1 3.53E-06 Lymph
node 1099358 FLJ39971 4.09E-06 Lymph node 1130509 SPARC 6.23E-06
Lymph node 1095985 TMEPAI 7.07E-06 Lymph node 1123038 ACTN1
7.90E-06 Lymph node 1133700 CDH11 8.20E-06 Lymph node 1122101 TFEC
9.66E-06 Lymph node 1124296 SDC2 9.99E-06 MHC Class II 1123127
HLA-DRA 1.21E-06 MHC Class II 1136777 HLA-DQA1 3.45E-06 MHC Class
II 1137771 HLA-DRB1 3.95E-06 MHC Class II 1134281 HLA-DRB4 2.70E-05
MHC Class II 1136573 HLA-DPA1 2.92E-05 MHC Class II 1132710
HLA-DRB3 7.09E-05
[0214] Fitting the Cox proportional hazards model to the three gene
expression signature values resulted in the following model:
Survival predictor score=[0.586*(ABC DLBCL high gene expression
signature value)]-[0.468*(lymph node gene expression signature
value)]-[0.336*(MHC Class II gene expression signature value)].
A higher survival predictor score was associated with worse
outcome. According to a likelihood ratio test adjusted for the
number of variables included, this model was significant in
predicting survival at p=2.13.times.10.sup.-10. In order to
visualize the predictive power of the model, the 205 samples used
to create the model were ranked according to their survival
predictor scores and divided into four quartiles, Kaplan-Meier
plots of overall survival probability show clear differences in
survival rate between these four quartiles (FIG. 10). The five-year
survival probabilities for each quartile are set forth in Table
2370.
TABLE-US-00014 TABLE 2370 Quartile 5-year survival 1 83% 2 59% 3
33% 4 17%
Example 7
Development of a Second DLBCL Survival Predictor Using Gene
Expression Data From the Lymph Dx Microarray
[0215] A DLBCL survival model: based on gene expression had been
developed previously using proliferation, germinal center B-cell,
lymph node, and MHC class II gene expression signatures and the
expression of the single gene BMP-6 (Rosenwald 2002). BMP-6
expression was poorly measured on the Lymph Dx microarray, but
genes associated with each of these four gene expression signatures
exhibited associations with survival similar to those observed
using Lymphochip microarrays. DLBCL samples were divided into two
groups: a training set (100 samples) for developing the survival
prediction model, and a validation set (100 samples) for evaluating
the reproducibility of the model. Gene expressed in the training
set samples were clustered, and lymph node, germinal center B-cell,
MHC class II, and proliferation gene expression signatures were
identified. Within each signature, expression of genes that were
associated with survival (p<0.01) was averaged to generate a
gene expression signature value for each signature. Table 2371
lists the genes that were used to generate the gene expression
signature value for each signature.
TABLE-US-00015 TABLE 2371 Unigene ID Build 167 Signature UNIQID
(http://www.ncbi.nlm.nih.gov/UniGene) Gene symbol Germinal center
B-cell 1099686 117721 Germinal center B-cell 1099711 243596
Germinal center B-cell 1103390 271752 BPNT1 Germinal center B-cell
1106025 49500 KIAA0746 Germinal center B-cell 1128287 300063 ASB13
Germinal center B-cell 1132520 283063 LMO2 Germinal center B-cell
1138192 126608 NR3C1 Germinal center B-cell 1529318 291954 Germinal
center B-cell 1529344 317970 SERPINA11 Germinal center B-cell
1529352 446195 Germinal center B-cell 1096570 409813 ANUBL1
Germinal center B-cell 1097897 266175 PAG Germinal center B-cell
1097901 266175 PAG Germinal center B-cell 1098611 433611 PDK1
Germinal center B-cell 1100581 155024 BCL6 Germinal center B-cell
1115034 387222 NEK6 Germinal center B-cell 1120090 155024 BCL6
Germinal center B-cell 1120946 25209 MAPK10 Germinal center B-cell
1121248 54089 BARD1 Germinal center B-cell 1123105 434281 PTK2
Germinal center B-cell 1125456 300592 MYBL1 Germinal center B-cell
1128694 171466 ELL3 Germinal center B-cell 1128787 114611 C7orf10
Germinal center B-cell 1132122 307734 MME Germinal center B-cell
1136269 101474 MAST2 Germinal center B-cell 1136702 155584 KIAA0121
Germinal center B-cell 1139230 29724 PLEKHF2 Germinal center B-cell
1529292 NA Germinal center B-cell 1529295 116441 Lymph node 1097126
274520 ANTXR1 Lymph node 1099028 334838 FNDC1 Lymph node 1099358
93135 Lymph node 1101478 146246 MGC45780 Lymph node 1103497 50115
Lymph node 1121029 412999 CSTA Lymph node 1124429 409602 SULF1
Lymph node 1135068 71719 PDLIM3 Lymph node 1136051 520937 CSF2RA
Lymph node 1136172 38084 SULT1C1 MHC class II 1136777 387679
HLA-DQA1 MHC class II 1136877 409934 HLA-DQB1 Proliferation 1096903
437460 FLJ10385 Proliferation 1120583 153768 RNU3IP2 Proliferation
1123289 5409 POLR1C Proliferation 1131808 75447 RALBP1
Proliferation 1133102 360041 FRDA Proliferation 1136595 404814
VDAC1
[0216] Table 2372 lists p-values for the association of each
signature with survival in the training set, the validation set,
and overall.
TABLE-US-00016 TABLE 2372 Signature Training set Validation set
Overall Lymph node 4.0 .times. 10.sup.-5 2.3 .times. 10.sup.-6
.sup. 6.8 .times. 10.sup.-10 Proliferation 8.1 .times. 10.sup.-5
3.4 .times. 10.sup.-3 2.1 .times. 10.sup.-6 Germinal center B-cell
6.2 .times. 10.sup.-6 2.1 .times. 10.sup.-3 5.0 .times. 10.sup.-8
MHC class II 2.4 .times. 10.sup.-2 2.7 .times. 10.sup.-3 3.1
.times. 10.sup.-4
[0217] The four gene expression signatures were used to generate a
survival predictor score using the following equation:
Survival predictor score=[-0.4337*(lymph node gene expression
signature value)]+[0.09*(proliferation gene expression signature
value)]-[0.4144*(germinal center B-cell gene expression signature
value)]-[0.2006*(MHC class II gene expression signature
value)].
A higher survival predictor score was associated with worse
outcome. For the 200 DLBCL samples used to generate the model, the
survival predictor score had a mean of 5.7 and a standard deviation
of 0.78, with each unit increase in the predictor score
corresponding to an approximately 2.7 fold increase in the relative
risk of death. Data for all 200 samples is presented in Table
2373.
TABLE-US-00017 TABLE 2373 Germinal Lymph center B- MHC node
Proliferation cell class II Survival signature signature signature
signature predictor Sample ID # Set value value value value score
ABC_1000 Validation 6.50 8.92 7.60 11.50 -5.08 ABC_1002 Validation
7.00 8.58 7.27 12.54 -5.50 ABC_1023 Validation 7.43 8.99 6.80 11.42
-5.05 ABC_1027 Training 5.68 9.00 6.87 12.31 -4.70 ABC_1031
Validation 8.02 9.00 7.17 11.68 -5.53 ABC_1034 Validation 6.06 9.61
6.72 11.83 -4.58 ABC_1038 Training 6.83 8.97 7.17 12.30 -5.23
ABC_1043 Training 6.96 9.01 6.77 12.29 -5.11 ABC_1045 Validation
8.18 8.21 6.77 12.07 -5.66 ABC_1055 Validation 5.58 9.16 7.30 13.05
-4.76 ABC_1057 Training 7.33 8.94 7.74 12.05 -5.53 ABC_1059
Validation 9.02 8.46 7.15 11.35 -6.08 ABC_1061 Training 7.13 9.18
7.09 12.28 -5.21 ABC_304 Validation 5.92 8.80 6.78 12.76 -4.84
ABC_305 Training 5.92 8.74 7.50 11.89 -4.91 ABC_309 Validation 8.86
8.39 7.62 12.53 -6.46 ABC_413 Validation 6.45 9.32 6.55 9.04 -4.16
ABC_428 Training 7.52 9.19 7.98 10.25 -5.51 ABC_432 Validation 6.48
9.33 7.45 9.56 -4.56 ABC_446 Training 7.91 9.42 7.41 10.55 -5.46
ABC_462 Validation 6.41 8.85 6.67 13.36 -5.03 ABC_477 Validation
6.26 9.02 6.69 12.45 -4.89 ABC_481 Training 8.18 8.30 7.35 11.98
-5.91 ABC_482 Training 8.59 9.01 7.66 12.35 -6.16 ABC_538
Validation 8.06 8.84 7.17 11.83 -5.69 ABC_541 Training 6.14 8.52
7.42 10.59 -4.71 ABC_544 Training 6.91 9.03 6.82 11.87 -4.89
ABC_547 Validation 5.80 8.96 7.14 11.38 -4.60 ABC_577 Validation
7.84 8.65 8.16 11.95 -5.94 ABC_616 Validation 6.03 9.05 7.36 12.64
-4.84 ABC_626 Validation 7.48 9.22 7.25 11.11 -5.27 ABC_633
Training 7.74 8.35 7.39 12.45 -5.80 ABC_642 Training 5.71 8.82 6.41
13.80 -4.62 ABC_644 Validation 6.64 9.15 7.05 13.28 -5.20 ABC_645
Training 8.44 8.81 7.93 13.39 -6.43 ABC_646 Validation 5.94 9.11
6.71 11.60 -4.63 ABC_652 Validation 5.87 8.85 6.88 12.73 -4.77
ABC_660 Training 5.19 9.34 6.64 10.17 -3.86 ABC_663 Training 5.69
9.02 7.33 12.82 -4.91 ABC_668 Validation 7.12 9.28 7.03 10.57 -4.91
ABC_676 Training 4.95 8.90 7.09 13.32 -4.61 ABC_678 Training 5.84
9.11 7.34 11.26 -4.41 ABC_687 Validation 5.15 9.89 6.56 10.46 -3.76
ABC_689 Training 6.49 8.86 7.10 12.56 -4.88 ABC_692 Validation 7.32
8.96 7.25 11.57 -5.32 ABC_694 Validation 8.28 9.21 8.01 12.41 -6.23
ABC_700 Training 7.29 8.97 7.55 12.10 -5.48 ABC_702 Validation 7.60
8.66 6.86 12.55 -5.45 ABC_704 Training 7.07 8.92 7.03 12.83 -5.35
ABC_709 Validation 5.92 8.58 6.37 13.40 -4.66 ABC_712 Validation
5.79 9.12 6.34 12.02 -4.23 ABC_714 Training 7.49 8.88 7.49 11.97
-5.54 ABC_717 Training 7.17 9.45 7.01 11.34 -5.05 ABC_725 Training
6.71 9.01 6.52 12.76 -4.86 ABC_726 Validation 6.91 8.72 6.71 11.91
-4.90 ABC_730 Validation 6.28 9.22 7.28 12.14 -4.88 ABC_753
Training 8.84 9.64 7.05 13.00 -5.22 ABC_756 Training 7.67 8.45 7.59
12.48 -5.85 ABC_771 Training 6.98 8.76 6.91 12.20 -5.18 ABC_779
Training 6.73 9.32 6.78 9.82 -4.44 ABC_800 Validation 8.75 8.31
7.45 11.91 -6.04 ABC_807 Training 5.50 9.53 6.92 7.56 -3.79 ABC_809
Training 7.40 8.70 7.68 10.83 -5.50 ABC_816 Training 5.20 9.91 7.65
10.64 -4.14 ABC_820 Training 6.71 8.94 6.55 11.98 -4.85 ABC_823
Validation 5.58 9.26 6.44 10.09 -3.97 ABC_835 Validation 6.95 8.68
8.04 12.31 -5.59 ABC_839 Training 6.63 9.17 7.23 11.89 -5.04
ABC_841 Validation 6.35 9.51 7.52 13.19 -5.28 ABC_858 Training 7.63
8.51 7.12 11.74 -5.42 ABC_872 Training 6.78 8.73 7.41 12.47 -5.44
ABC_875 Training 7.59 8.81 7.20 11.26 -5.25 ABC_912 Validation 7.01
8.55 7.45 12.79 -5.64 ABC_996 Validation 5.00 9.53 6.70 10.02 -3.94
GCB_1005 Validation 8.28 8.67 9.11 13.27 -6.98 GCB_1008 Training
8.17 8.59 9.83 12.83 -7.06 GCB_1009 Training 6.63 9.02 10.07 12.28
-6.19 GCB_1021 Validation 6.44 8.83 9.34 13.20 -6.15 GCB_1025
Validation 7.87 8.48 9.27 12.37 -6.57 GCB_1026 Training 7.71 8.30
9.81 13.52 -6.85 GCB_1037 Training 4.95 8.83 9.35 12.57 -5.22
GCB_1039 Training 7.63 8.65 9.01 13.28 -6.47 GCB_1049 Validation
8.54 8.61 8.12 12.60 -6.41 GCB_1051 Validation 6.26 9.09 9.48 12.76
-5.97 GCB_1058 Validation 7.12 8.89 8.34 12.80 -5.85 GCB_1060
Validation 8.27 8.84 8.94 12.96 -6.75 GCB_412 Training 7.22 8.33
8.50 13.09 -6.09 GCB_415 Training 9.01 8.62 8.38 11.99 -6.47
GCB_421 Training 7.59 7.89 7.49 12.20 -5.80 GCB_424 Training 9.29
8.42 8.51 12.44 -6.79 GCB_433 Training 8.45 8.34 8.02 12.64 -6.54
GCB_434 Training 8.46 8.55 9.17 12.54 -6.98 GCB_438 Validation 8.14
8.71 9.13 12.51 -6.67 GCB_459 Validation 8.98 8.39 8.42 11.37 -6.49
GCB_470 Validation 7.72 8.57 8.67 12.23 -6.12 GCB_479 Validation
6.86 8.25 7.13 13.07 -5.35 GCB_492 Training 8.01 8.61 9.51 12.34
-6.63 GCB_517 Validation 8.57 8.73 7.99 12.76 -6.48 GCB_523
Training 5.96 8.56 8.74 12.77 -5.72 GCB_524 Training 8.51 8.09 8.76
12.51 -6.57 GCB_529 Training 5.12 9.17 8.88 10.77 -4.86 GCB_533
Training 8.88 8.81 8.36 12.44 -6.60 GCB_537 Validation 7.42 8.19
9.73 13.29 -6.68 GCB_543 Validation 8.49 8.02 8.66 12.08 -6.45
GCB_545 Training 8.65 8.28 6.90 12.90 -6.13 GCB_549 Validation 6.87
8.24 8.65 12.15 -6.00 GCB_550 Validation 8.98 8.29 8.76 12.24 -6.94
GCB_553 Validation 8.51 8.64 8.62 12.63 -6.69 GCB_565 Validation
7.97 8.79 9.79 13.42 -6.98 GCB_572 Training 7.61 8.60 9.39 12.58
-6.42 GCB_617 Validation 8.31 7.89 7.54 13.17 -6.12 GCB_618
Training 5.66 8.97 9.20 13.32 -5.54 GCB_619 Validation 7.83 8.65
9.34 12.12 -6.36 GCB_623 Training 7.16 8.88 9.26 12.35 -6.21
GCB_627 Validation 8.13 8.83 8.62 11.85 -6.31 GCB_654 Training 6.30
9.60 8.45 10.00 -4.88 GCB_661 Validation 8.46 8.51 8.18 12.66 -6.33
GCB_669 Training 7.88 8.65 8.59 12.32 -6.19 GCB_672 Training 8.29
8.61 8.14 12.41 -6.21 GCB_674 Validation 8.36 8.62 7.76 12.33 -6.14
GCB_675 Validation 6.01 9.52 8.90 10.12 -5.09 GCB_681 Training 9.25
8.72 8.72 12.59 -6.89 GCB_688 Validation 6.97 9.01 9.90 9.94 -5.99
GCB_695 Validation 8.80 8.73 9.23 12.45 -6.84 GCB_698 Validation
9.27 8.35 8.85 11.99 -6.96 GCB_701 Training 7.77 7.93 8.68 13.10
-6.33 GCB_710 Validation 6.12 8.78 7.65 13.19 -5.24 GCB_711
Training 7.57 8.80 8.43 11.44 -5.84 GCB_722 Training 7.78 8.31 8.93
12.61 -6.51 GCB_724 Training 7.88 9.08 8.74 11.53 -6.21 GCB_731
Validation 7.72 8.92 9.08 12.20 -6.46 GCB_742 Validation 8.33 8.55
8.58 12.95 -6.70 GCB_744 Training 8.02 8.64 9.36 11.85 -6.52
GCB_745 Training 8.47 8.34 8.93 11.95 -6.67 GCB_747 Validation 7.64
8.48 8.32 13.06 -6.27 GCB_749 Training 7.57 8.61 9.40 12.55 -6.56
GCB_758 Validation 5.66 8.77 7.89 12.51 -4.63 GCB_772 Validation
8.52 7.81 7.95 12.25 -6.34 GCB_777 Validation 7.52 8.65 8.57 11.69
-6.10 GCB_792 Training 8.14 8.64 9.21 12.08 -6.65 GCB_795
Validation 9.19 8.17 8.81 11.60 -6.92 GCB_797 Validation 7.50 8.62
8.08 12.84 -6.09 GCB_803 Validation 6.19 8.65 9.49 13.18 -6.11
GCB_810 Training 8.46 8.32 8.10 13.13 -6.50 GCB_817 Training 6.93
8.51 9.49 11.09 -6.04 GCB_818 Training 7.18 8.96 8.08 12.23 -5.76
GCB_819 Validation 7.16 8.97 8.06 13.22 -5.79 GCB_821 Validation
8.13 8.59 8.90 12.41 -6.61 GCB_832 Training 7.83 8.35 8.71 12.47
-6.37 GCB_836 Validation 7.84 8.99 8.50 11.46 -5.85 GCB_840
Training 8.24 7.75 7.40 11.74 -5.77 GCB_847 Training 7.82 8.17 8.97
12.55 -6.51 GCB_860 Training 7.12 8.39 9.34 11.54 -6.10 GCB_871
Training 5.59 9.60 7.28 11.16 -4.23 GCB_874 Training 8.53 9.14 8.95
11.65 -6.47 GCB_995 Validation 6.98 8.68 8.54 12.22 -5.76 PMBL_1006
Validation 7.34 8.51 7.66 10.94 -5.33 PMBL_1024 Validation 7.62
8.48 8.56 10.89 -5.96 PMBL_1048 Validation 8.68 8.16 7.23 12.18
-6.08 PMBL_1053 Training 7.02 8.28 8.24 11.12 -5.31 PMBL_484
Training 7.15 8.45 7.01 13.62 -5.41 PMBL_546 Validation 8.19 7.88
7.66 11.73 -6.06 PMBL_570 Training 9.34 8.21 8.48 12.70 -6.86
PMBL_621 Training 8.08 8.60 9.14 12.96 -6.72 PMBL_638 Training 7.56
8.26 8.00 11.37 -5.75 PMBL_691 Validation 6.48 8.92 8.40 10.17
-5.04 PMBL_791 Validation 7.72 8.65 8.94 11.56 -6.16 PMBL_824
Validation 8.06 8.01 7.76 13.28 -6.11 PMBL_994 Training 9.15 8.36
7.46 12.43 -6.29 PMBL_998 Training 6.70 8.35 9.24 13.19 -6.20
UC_DLBCL_1001 Validation 6.74 8.43 7.10 12.76 -5.31 UC_DLBCL_1004
Validation 7.54 8.75 8.01 13.09 -6.10 UC_DLBCL_1007 Training 9.97
8.44 7.64 12.97 -6.85 UC_DLBCL_1018 Training 6.42 8.38 6.97 12.71
-5.03 UC_DLBCL_1041 Validation 5.76 8.69 6.78 13.36 -4.71
UC_DLBCL_1054 Training 8.92 8.65 8.51 11.48 -6.59 UC_DLBCL_306
Validation 7.85 8.90 8.31 12.36 -6.23 UC_DLBCL_310 Training 8.14
8.80 7.63 12.27 -6.03 UC_DLBCL_449 Validation 9.03 8.48 7.07 12.17
-6.01 UC_DLBCL_458 Training 5.92 8.53 8.28 9.60 -4.96 UC_DLBCL_460
Validation 7.92 9.08 8.30 12.29 -6.13 UC_DLBCL_491 Training 7.65
8.33 7.35 12.39 -5.53 UC_DLBCL_528 Validation 6.99 8.56 7.36 11.63
-5.35 UC_DLBCL_615 Validation 7.11 8.32 8.77 12.80 -6.10
UC_DLBCL_625 Training 8.93 7.78 7.85 12.62 -6.46 UC_DLBCL_664
Training 7.62 8.15 8.17 12.72 -6.04 UC_DLBCL_671 Training 8.09 8.48
7.61 11.53 -5.78 UC_DLBCL_682 Training 7.38 8.35 7.14 12.33 -5.43
UC_DLBCL_683 Training 7.91 8.36 7.78 12.57 -6.02 UC_DLBCL_684
Validation 8.06 8.63 8.29 12.76 -6.29 UC_DLBCL_748 Validation 5.38
8.57 7.45 9.55 -4.23 UC_DLBCL_751 Training 6.33 8.65 8.88 13.14
-5.74 UC_DLBCL_808 Training 7.42 9.01 7.44 13.09 -5.63 UC_DLBCL_831
Validation 8.33 8.30 7.46 11.58 -5.84 UC_DLBCL_834 Training 6.98
9.09 8.61 11.77 -5.66 UC_DLBCL_838 Validation 7.25 8.40 7.23 12.56
-5.36 UC_DLBCL_851 Validation 6.28 9.05 6.78 8.19 -4.10
UC_DLBCL_854 Validation 7.36 8.50 7.39 12.59 -5.53 UC_DLBCL_855
Training 8.31 7.94 7.49 12.08 -6.07 UC_DLBCL_856 Validation 5.65
9.01 8.52 9.32 -4.68
[0218] In order to visualize the predictive power of the model, the
200 samples were ranked according to their survival predictor
scores and divided into four quartiles. Kaplan-Meier plots of
overall survival probability show clear differences in survival
rate between these four quartiles (FIG. 11).
Example 8
Development of a Third DLBCL Survival Predictor Using Gene
Expression Data From the Lymph Dx Microarray
[0219] The number of genes used to generate the DLBCL survival
predictor in Example 7 was reduced in order to create a survival
predictor compatible with RT-PCR. The list of genes from the lymph
node and germinal center B-cell gene expression signatures was
narrowed to those three genes from each signature that were most
closely correlated with the lymph node and germinal center B-cell
gene expression signature values, respectively. The genes from the
proliferation gene expression signature did not add significantly
to the reduced gene survival prediction model, so they were removed
entirely. The expression of genes within each signature was
averaged on the logs scale to generate a gene expression signature
value for each signature. Table 2374 lists the genes that were used
to generate these gene expression signature values.
TABLE-US-00018 TABLE 2374 Unigene ID Build 167 Signature UNIQID
http://www.ncbi.nlm.nih.gov/UniGene Gene symbol Germinal center
B-cell 1099686 117721 Germinal center B-cell 1529318 291954
Germinal center B-cell 1529344 317970 SERPINA11 Lymph node 1097126
274520 ANTXR1 Lymph node 1099358 93135 Lymph node 1121029 412999
CSTA MHC class II 1136777 387679 HLA-DQA1 MHC class II 1136877
409934 HLA-DQB1
[0220] Table 2376 lists p-values for association of each signature
with survival in the training set, the validation set, and
overall.
TABLE-US-00019 TABLE 2375 Signature Training set Validation set
Overall Lymph node 6.1 .times. 10.sup.-6 0.0021 2.1 .times.
10.sup.-17 Germinal center B-cell 3.5 .times. 10.sup.-4 0.0099 2.7
.times. 10.sup.-5 MHC class II 0.024 0.0026 0.00031
[0221] The three gene expression signatures were used to generate a
survival predictor score using the following equation:
Survival predictor score=[-0.32*(lymph node gene expression
signature value)]-[0.176*(germinal center B-cell gene expression
signature value)]-0.206*(MHC class II gene expression signature
value)].
A higher survival predictor score was associated with worse
outcome. For the 200 DLBCL samples used to generate the model, the
survival predictor score had a mean of 6.54 and a standard
deviation of 0.69, with each unit increase in the predictor score
corresponding to an approximately 2.7 fold increase in the relative
risk of death. Data for all 200 samples is presented in Table
2376.
TABLE-US-00020 TABLE 2376 Lymph Germinal MHC node center class II
Survival signa- B-cell signa- pre- Sample ture signature ture
dictor ID # Set value value value score ABC_1000 Validation 8.08
5.68 11.50 -5.96 ABC_1002 Validation 8.32 6.06 12.54 -6.31 ABC_1023
Validation 9.36 4.74 11.42 -6.18 ABC_1027 Training 7.41 4.90 12.31
-5.77 ABC_1031 Validation 9.40 5.23 11.68 -6.33 ABC_1034 Validation
7.47 4.92 11.83 -5.69 ABC_1038 Training 7.89 5.84 12.30 -6.09
ABC_1043 Training 7.84 4.66 12.29 -5.86 ABC_1045 Validation 9.31
4.66 12.07 -6.29 ABC_1055 Validation 6.46 6.38 13.05 -5.88 ABC_1057
Training 9.13 7.93 12.05 -6.80 ABC_1059 Validation 10.93 4.82 11.35
-6.68 ABC_1061 Training 8.18 5.04 12.28 -6.04 ABC_304 Validation
7.31 6.47 12.76 -6.10 ABC_305 Training 7.02 6.60 11.89 -5.86
ABC_309 Validation 10.47 7.00 12.53 -7.16 ABC_413 Validation 7.99
4.80 9.04 -5.26 ABC_428 Training 9.43 7.59 10.25 -6.47 ABC_432
Validation 7.29 8.16 9.56 -5.74 ABC_446 Training 9.49 5.46 10.55
-6.17 ABC_462 Validation 7.72 4.97 13.36 -6.10 ABC_477 Validation
7.16 3.69 12.45 -5.51 ABC_481 Training 9.75 6.89 11.98 -6.80
ABC_482 Training 10.51 7.64 12.35 -7.25 ABC_538 Validation 8.79
5.00 11.83 -6.13 ABC_541 Training 7.70 5.80 10.59 -5.67 ABC_544
Training 8.90 3.98 11.87 -5.99 ABC_547 Validation 7.05 5.18 11.38
-5.51 ABC_577 Validation 9.93 8.05 11.95 -7.06 ABC_616 Validation
7.34 4.54 12.64 -5.75 ABC_626 Validation 8.78 6.77 11.11 -6.29
ABC_633 Training 9.63 5.02 12.45 -6.53 ABC_642 Training 7.31 4.95
13.80 -6.05 ABC_644 Validation 7.72 5.35 13.28 -6.15 ABC_645
Training 9.77 6.21 13.39 -6.98 ABC_646 Validation 7.39 3.75 11.60
-5.41 ABC_652 Validation 7.51 4.53 12.73 -5.82 ABC_660 Training
5.85 3.55 10.17 -4.59 ABC_663 Training 7.04 5.06 12.82 -5.78
ABC_668 Validation 8.00 5.65 10.57 -5.73 ABC_676 Training 6.53 4.29
13.32 -5.59 ABC_678 Training 6.87 7.48 11.26 -5.83 ABC_687
Validation 6.39 3.78 10.46 -4.87 ABC_689 Training 8.29 5.07 12.56
-6.13 ABC_692 Validation 8.10 5.26 11.57 -5.90 ABC_694 Validation
9.67 8.15 12.41 -7.09 ABC_700 Training 8.37 6.75 12.10 -6.36
ABC_702 Validation 8.44 4.59 12.55 -6.09 ABC_704 Training 8.51 4.34
12.83 -6.13 ABC_709 Validation 7.47 4.54 13.40 -5.95 ABC_712
Validation 7.12 3.99 12.02 -5.46 ABC_714 Training 9.57 7.03 11.97
-6.77 ABC_717 Training 8.33 5.54 11.34 -5.98 ABC_725 Training 8.04
4.40 12.76 -5.97 ABC_726 Validation 7.79 4.18 11.91 -5.68 ABC_730
Validation 8.13 7.36 12.14 -6.40 ABC_753 Training 9.24 6.60 13.00
-6.80 ABC_756 Training 9.51 5.21 12.48 -6.53 ABC_771 Training 8.08
4.74 12.20 -5.93 ABC_779 Training 8.11 4.09 9.82 -5.34 ABC_800
Validation 10.34 4.83 11.91 -6.61 ABC_807 Training 6.58 4.44 7.56
-4.44 ABC_809 Training 9.29 5.72 10.83 -6.21 ABC_816 Training 6.36
6.36 10.64 -5.35 ABC_820 Training 8.10 4.79 11.98 -5.90 ABC_823
Validation 6.63 4.85 10.09 -5.05 ABC_835 Validation 9.17 7.78 12.31
-6.84 ABC_839 Training 8.06 4.97 11.89 -5.90 ABC_841 Validation
8.05 6.24 13.19 -6.39 ABC_858 Training 9.02 4.86 11.74 -6.16
ABC_872 Training 8.67 5.85 12.47 -6.37 ABC_875 Training 9.60 5.59
11.26 -6.37 ABC_912 Validation 7.99 7.74 12.79 -6.56 ABC_996
Validation 6.89 6.23 10.02 -5.36 GCB_1005 Validation 9.02 9.56
13.27 -7.30 GCB_1008 Training 9.27 10.49 12.83 -7.46 GCB_1009
Training 7.80 10.09 12.28 -6.80 GCB_1021 Validation 8.73 9.20 13.20
-7.13 GCB_1025 Validation 9.94 9.97 12.37 -7.49 GCB_1026 Training
9.54 10.20 13.52 -7.63 GCB_1037 Training 6.34 8.79 12.57 -6.17
GCB_1039 Training 8.71 9.94 13.28 -7.27 GCB_1049 Validation 10.53
8.18 12.60 -7.41 GCB_1051 Validation 7.63 10.18 12.76 -6.86
GCB_1058 Validation 8.61 9.04 12.80 -6.98 GCB_1060 Validation 10.23
9.38 12.96 -7.59 GCB_412 Training 8.79 7.92 13.09 -6.90 GCB_415
Training 10.72 8.57 11.99 -7.41 GCB_421 Training 9.23 5.26 12.20
-6.39 GCB_424 Training 11.14 8.46 12.44 -7.62 GCB_433 Training 9.26
8.52 12.64 -7.07 GCB_434 Training 9.73 10.13 12.54 -7.48 GCB_438
Validation 9.60 9.99 12.51 -7.41 GCB_459 Validation 10.51 7.75
11.37 -7.07 GCB_470 Validation 9.56 6.63 12.23 -6.74 GCB_479
Validation 7.77 4.71 13.07 -6.01 GCB_492 Training 8.82 9.52 12.34
-7.04 GCB_517 Validation 9.92 6.96 12.76 -7.03 GCB_523 Training
6.59 9.17 12.77 -6.35 GCB_524 Training 10.00 7.83 12.51 -7.16
GCB_529 Training 5.61 7.93 10.77 -5.41 GCB_533 Training 9.55 5.54
12.44 -6.59 GCB_537 Validation 8.25 10.25 13.29 -7.18 GCB_543
Validation 9.92 8.85 12.06 -7.21 GCB_545 Training 9.69 4.91 12.90
-6.62 GCB_549 Validation 7.86 8.88 12.15 -6.58 GCB_550 Validation
10.64 9.53 12.24 -7.60 GCB_553 Validation 10.14 9.05 12.63 -7.44
GCB_565 Validation 9.08 10.80 13.42 -7.57 GCB_572 Training 8.93
10.03 12.58 -7.21 GCB_617 Validation 9.27 7.80 13.17 -7.05 GCB_618
Training 7.23 9.11 13.32 -6.66 GCB_619 Validation 9.63 9.63 12.12
-7.27 GCB_623 Training 8.94 9.07 12.35 -7.00 GCB_627 Validation
9.72 8.33 11.85 -7.02 GCB_654 Training 7.04 5.60 10.00 -5.30
GCB_661 Validation 10.27 7.92 12.66 -7.29 GCB_669 Training 9.15
9.29 12.32 -7.10 GCB_672 Training 9.69 7.36 12.41 -6.95 GCB_674
Validation 9.93 6.23 12.33 -6.81 GCB_675 Validation 7.48 8.46 10.12
-5.97 GCB_681 Training 10.77 9.52 12.59 -7.72 GCB_688 Validation
8.01 10.17 9.94 -6.40 GCB_695 Validation 10.58 9.38 12.45 -7.60
GCB_698 Validation 10.44 9.00 11.99 -7.39 GCB_701 Training 9.38
9.27 13.10 -7.33 GCB_710 Validation 6.96 5.59 13.19 -5.93 GCB_711
Training 9.28 8.49 11.44 -6.82 GCB_722 Training 8.93 9.51 12.61
-7.13 GCB_724 Training 9.51 8.39 11.53 -6.90 GCB_731 Validation
8.82 9.19 12.20 -6.95 GCB_742 Validation 9.95 9.37 12.95 -7.50
GCB_744 Training 10.23 10.11 11.85 -7.49 GCB_745 Training 10.29
9.71 11.95 -7.46 GCB_747 Validation 9.83 9.79 13.06 -7.56 GCB_749
Training 8.57 10.27 12.55 -7.14 GCB_758 Validation 6.88 5.69 12.51
-5.78 GCB_772 Validation 9.92 7.28 12.25 -6.98 GCB_777 Validation
9.03 9.63 11.69 -6.99 GCB_792 Training 9.49 9.06 12.08 -7.12
GCB_795 Validation 11.12 9.02 11.60 -7.54 GCB_797 Validation 8.42
5.90 12.84 -6.38 GCB_803 Validation 7.33 10.11 13.18 -6.84 GCB_810
Training 10.00 8.22 13.13 -7.35 GCB_817 Training 8.60 10.16 11.09
-6.82 GCB_818 Training 9.14 7.78 12.23 -6.81 GCB_819 Validation
9.08 8.63 13.22 -7.15 GCB_821 Validation 10.05 9.81 12.41 -7.50
GCB_832 Training 8.83 6.91 12.47 -6.61 GCB_836 Validation 9.49 7.86
11.46 -6.78 GCB_840 Training 9.45 5.02 11.74 -6.33 GCB_847 Training
9.41 8.77 12.55 -7.14 GCB_860 Training 9.02 6.66 11.54 -6.43
GCB_871 Training 6.60 4.46 11.16 -5.20 GCB_874 Training 10.39 9.13
11.65 -7.33 GCB_995 Validation 8.52 9.35 12.22 -6.89 PMBL_1006
Validation 8.72 4.67 10.94 -5.86 PMBL_1024 Validation 9.30 8.47
10.89 -6.71 PMBL_1048 Validation 10.30 4.98 12.18 -6.68 PMBL_1053
Training 8.75 9.78 11.12 -6.81 PMBL_484 Training 8.25 4.96 13.62
-6.32 PMBL_546 Validation 9.66 6.07 11.73 -6.57 PMBL_570 Training
10.58 8.54 12.70 -7.50 PMBL_621 Training 9.39 9.94 12.96 -7.43
PMBL_638 Training 9.81 8.35 11.37 -6.95 PMBL_691 Validation 8.37
7.51 10.17 -6.10 PMBL_791 Validation 9.29 8.65 11.56 -6.88 PMBL_824
Validation 9.87 7.19 13.28 -7.16 PMBL_994 Training 11.27 6.73 12.43
-7.35 PMBL_998 Training 7.92 8.34 13.19 -6.72 UC_DLBCL_1001
Validation 8.25 5.63 12.76 -6.26 UC_DLBCL_1004 Validation 9.01 7.01
13.09 -6.81 UC_DLBCL_1007 Training 11.42 6.73 12.97 -7.51
UC_DLBCL_1018 Training 7.77 4.58 12.71 -5.91 UC_DLBCL_1041
Validation 7.90 4.33 13.38 -6.05 UC_DLBCL_1054 Training 10.41 8.72
11.48 -7.23 UC_DLBCL_306 Validation 9.42 6.54 12.36 -6.71
UC_DLBCL_310 Training 9.97 5.50 12.27 -6.69 UC_DLBCL_449 Validation
10.01 5.37 12.17 -6.65 UC_DLBCL_458 Training 7.50 5.79 9.60 -5.40
UC_DLBCL_460 Validation 10.26 8.27 12.29 -7.27 UC_DLBCL_491
Training 9.43 4.73 12.39 -6.40 UC_DLBCL_528 Validation 8.42 6.19
11.63 -6.18 UC_DLBCL_615 Validation 8.44 9.01 12.80 -6.92
UC_DLBCL_625 Training 10.43 8.27 12.62 -7.39 UC_DLBCL_664 Training
9.80 8.74 12.72 -7.29 UC_DLBCL_671 Training 9.42 5.26 11.53 -6.32
UC_DLBCL_682 Training 9.01 4.73 12.33 -6.26 UC_DLBCL_683 Training
8.85 8.23 12.57 -6.87 UC_DLBCL_684 Validation 9.62 8.78 12.76 -7.25
UC_DLBCL_748 Validation 7.60 5.79 9.55 -5.42 UC_DLBCL_751 Training
6.40 9.91 13.14 -6.50 UC_DLBCL_808 Training 9.44 7.01 13.09 -6.95
UC_DLBCL_831 Validation 9.45 5.81 11.58 -6.43 UC_DLBCL_834 Training
8.52 7.66 11.77 -6.50 UC_DLBCL_838 Validation 8.49 4.60 12.56 -6.11
UC_DLBCL_851 Validation 7.50 4.82 8.19 -4.94 UC_DLBCL_854
Validation 8.35 5.82 12.59 -6.29 UC_DLBCL_855 Training 9.56 5.44
12.08 -6.51 UC_DLBCL_856 Validation 6.81 7.49 9.32 -5.42
[0222] In order to visualize the predictive power of the model, the
200 samples were ranked according to their survival predictor
scores and divided into four quartiles. Kaplan-Meier plots of
overall survival probability show clear differences in survival
rate between these four quartiles (FIG. 12).
Example 9
Development of a Refined DLBCL Survival Predictor Based on Genomic
Alterations
[0223] Comparative genomic hybridization (CGH) was performed on 224
DLBCL samples for which gene expression profiles had previously
been obtained using a Lymphochip (Rosenwald 2002). Of these 224
samples, 87 had been classified as GCB based on the Lymphochip
expression data, 77 had been classified as ABC, 19 had been
classified as PMBL, and 41 were unclassified (Wright 2003).
Clinical data was available for each subject from whom the samples
had been obtained (Rosenwald 2002). All patients had received
anthracycllne-based chemotherapy. Median follow-up was 2.7 years
and 58% of patients died during this period. The median age of the
patients was 60 years and 54% were men 16% of patients had Ann
Arbor stage I disease and 30%, 19%, and 35% had Stage II, III, and
IV, respectively. 38% of DLBCL patients (78 cases) with available
data were in the low-risk IPI group (IPI 0-1), 48% (99 cases) were
in the intermediate-risk IPI group (IPI 2-3), and 14% (30 cases)
were in the high-risk IPI group (IPI 4-5).
[0224] CGH was carried out using a commercially available felt
(Vysis. Downers Grove, Ill.). Hybridization and digital image
acquisition, processing, and evaluation were performed on a
Cytovision Ultra workstation (Applied Imaging, Sunderland, UK) as
described previously (Bea 1999). Signal ratios greater than 1.25
were considered chromosomal gains, while signal ratios less than
0.75 were considered chromosomal losses. Ratios exceeding 1.5
and/or strong focal signals with a ratio profile showing
over-representation were considered genomic amplifications. All CGH
data are available at http://www.ncbi.nlm.nih.gov/sky.
[0225] CGH alterations in individual cytobands were treated as
categorical variables and their associations with DLBCL subgroups
or gene: expression signatures were analyzed as follows.
Preliminary analyses did not reveal significant differences in the
effects of gains and amplifications, so they were treated as
equivalent chromosomal abnormalities. Since a large number of
individual chromosomal abnormalities were analyzed, there was a
danger that some of the abnormalities would appear to be
significant purely by chance. To avoid such false positives, a
stepwise permutation test that generated nominal p-values
accounting for multiple hypothesis testing was used (Westfall 1993;
Simon 2003). This test takes into account the correlation between
different chromosomal abnormalities. Differences in abnormality
frequency between subtypes were detected using a chi squared test.
Differences in gene expression signature measures affected by
genomic imbalances were detected using a t-test. To further reduce
the effects of multiple comparisons, only those chromosomal
abnormalities that were present in a substantial portion of the
data were analyzed. For the subgroup analysis, only those
alterations that had a frequency of >20% in one or more of the
DLBCL subgroups were considered. For correlation with gene
expression signatures, chromosomal abnormalities were only
considered if they occurred in at least 5% of all DLBCL samples.
P-values for the association between gene expression levels (as a
continuous variable) and genomic imbalances (amplification vs. gain
vs. normal copy number) were calculated using an ANOVA test.
P-values of <0.01 were considered significant to account for
multiple comparisons. Overall survival was modeled using a Cox
proportional hazards approach and visualized using the Kaplan-Meier
method. The P values were adjusted for multiple comparisons, with
the follow-up time and status at follow-up being permuted. Once an
abnormality was found to be significant univariately, a likelihood
ratio test was used to determine whether this variable added
significantly to the survival model based on gene expression.
[0226] FIG. 29 shows the results of CGH analysis for GCB (A), ABC
(B), and PMBL (C) samples (Bea 2005). Overall, chromosomal
alterations were observed in 164 of the 224 patients (73%). A
summary of the most common alterations is set forth in Table
2415.
TABLE-US-00021 TABLE 2415 Un- classi- Overall ABC GCB PMBL fied (n
= 224) (n = 77) (n = 87) (n = 19) (n = 41) Samples 164 (73%) 63
(81%) 63 (72%) 16 (84%) 22 (54%) exhibiting alterations Mean 3.3
4.5 3.1 3.3 1.7 number of alterations Mean 1.9 2.5 1.6 2.1 1.0
number of gains Mean 0.3 0.4 0.3 0.4 0.0 number of amplifica- tions
Mean 1.2 1.6 1.1 0.8 0.6 number of losses Gains Xp 27 (12%) 12
(16%) 12 (14%) 3 (16%) 0 1q25-q32 26 (12%) 9 (12%) 9 (10%) 1 (5%) 7
(17%) 2p14-p16.sup.+ 39 (17%) 12 (15%) 15 (17%) 9 (47%) 3 (7%)
Trisomy 14 (6%) 12 (15%) 0 1 (5%) 1 (2%) 3.sup.+ 3p.sup.+ 28 (12%)
24 (31%) 1 (1%) 1 (5%) 2 (5%) 3q* 22 (10%) 20 (26%) 0 1 (5%) 1 (2%)
3q27-qter* 35 (16%) 26 (33%) 4 (5%) 3 (16%) 2 (5%) 6p 30 (13%) 13
(17%) 11 (13%) 1 (5%) 5 (12%) 7p 22 (10%) 8 (10%) 13 (15%) 1 (5%) 0
7q 25 (11%) 10 (13%) 13 (15%) 1 (5%) 1 (2%) 8q23-qter 23 (10%) 8
(10%) 10 (11%) .sup. 2 (11 %) 3 (7%) 9p* 14 (6%) 5 (6%) 0 7 (37%) 2
(5%) 12p 19 (8%) 4 (5%) 14 (16%) 1 (5%) 0 12q12.sup.# 24 (11%) 4
(5%) 18 (21%) 1 (5%) 1 (2%) 12q22-qter 22 (10%) 7 (9%) 13 (15%) 1
(5%) 1 (2%) 18q21- 42 (19%) 26 (34%) 9 (10%) 3 (16%) 4 (10%)
q22.sup.+ Losses 6q16 50 (22%) 26 (34%) 19 (22%) 0 5 (12%)
6q21-q22.sup.+ 55 (25%) 31 (40%) 19 (22%) 0 5 (12%) 8p22-pter 19
(8%) 8 (10%) 3 (3%) 3 (16%) 5 (12%) 17p 22 (10%) 14 (18%) 7 (8%) 0
1 (2%) *P < 0.001; .sup.+P < 0.05; .sup.#P = 0.059;
unclassified tumors were not included in statistical analysis
[0227] The number of alterations did not differ statistically
between GCB (3.1.+-.3.7, n=87), ABC (4.5.+-.4.5, n=77), PMBL
(3.3.+-.2.7, n=19) and unclassified DLBCL (1.7.+-.2.2, n=41). Among
samples exhibiting alterations, 81% exhibited more than one. The
most frequent alteration in those samples exhibiting only a single
alteration was loss of 6q (n=8), with two minimally lost regions in
6q21-q22 and 6q25-qter. These deletions may represent early events
in the development of these lymphomas.
[0228] Irrespective of the DLBCL subgroup, the most frequent
alterations were loss of 6q22-q22 (25%), loss of 6q16 (22%), gain
of 18q21-q22 (19%), gain of 2p14-p16 (47%), gain of 3q27-qter
(16%), gain of 6p (13%), and gain of Xp, 1q25-q32, and 3p (12%
each). Amplifications were identified in 33 different chromosomal
regions, most frequently in 2p14-p16 and 18q21-q22 (11 and 20
cases, respectively). Some alterations occurred frequently in the
same tumors, suggesting that they may be part of a recurrent
lymphogenesis pathway. For example, 17 of 26 ABC samples with
3q27-qter gains also exhibited 18q21-q22 gains (P=0.0001, odds
ratio: 9.23; 95% CI 3.14-27.2).
[0229] Notably, several chromosomal alterations were differentially
distributed among DLBCL subgroups (FIG. 29D). ABC exhibited
characteristic and recurrent gains of chromosome 3, gains and
amplification of 18q21-q22, and loss of 6q21-q22. Gains of the
whole 3q arm and trisomy 3, which were observed in 26% and 15% of
ABC samples, respectively, were never observed in GCB and observed
only once in PMBL. Gains of 18q21-q22 were observed in 34% of ABC
samples, versus only 10% and 16% of GCB and PMBL samples,
respectively. Amplification of 18q21, which contains the BCL2 gene,
was also more frequent in ABC (18%) than in GCB or PMBL (5% each).
Previous studies utilizing PCR-based and FISH methods found that
the t(14;18) translocation, which involves the BCL2 gene, occurs in
GCB but never in ABC (Huang 2002; Iqbal 2004). Interestingly, 3 of
the 4 GCB samples exhibiting amplification of 18q21 also exhibited
the t(14;18) translocation (the remaining case was not analyzed for
this translocation). High expression of the BCL2 gene is a
characteristic feature of ABC, but only occurs in GCB that have the
t(14;18) translocation (Alizadeh 2000; Huang 2002; Rosenwald 2002).
Together, these data suggest that amplification of the 18q21 region
occurs preferentially in lymphomas that have the ability to express
the BCL2 gene.
[0230] GCB samples were characterized by more frequent gains of
12q12 compared to ABC and PMBL, although this increase did not
reach statistical significance (21% for GCB vs. 5% for both ABC and
PMBL, P=0.059). PMBL samples were characterized by frequent gains
of 9p21-pter (37% for PMBL vs. 0% for GCB and 6% for ABC,
P<0.001) and 2p14-p16 (47% for PMBL vs, 17% for GCB and 11% for
ABC, P<0.02) compared to GCB and ABC. Taken together, these data
further demonstrate that GCB, ABC, and PMBL are genetically
distinct.
[0231] To confirm some of the more frequent DLBCL chromosomal
alterations identified by CGH, real-time quantitative PCR (RQ-PCR)
was used to quantify the copy number of select genes from the
following regions; 2p14-16 (REL, BCL11A), 12q13-q14 (SAS, CDK4,
MDM2), 3q27 (RFC4, BCL6, and 18q21 (MADH4, MALT1, BCL2). RQ-PCR was
performed using the ABI Prism 7700 Sequence Detector System
(Applied Biosystems). .beta..sub.2-microglobulin (.beta..sub.2M)
was used as a reference gene. Each assay was analyzed using the
comparative cycle threshold (C.sub.T) method, using the arithmetic
formula provided by the manufacturer. To determine the cut-off
values for a genomic gain/amplification in each probe set, eight
DNA samples from peripheral blood or placenta of healthy subjects
was studied. The cut-off value for a genomic gain was determined to
be the mean ratio plus three standard deviation units
(approximately 1.3 for each gene). A ratio between the cut-off
value and 2 was considered a gain, while a ratio of greater than 2
was considered an amplification. A subset of samples were also
investigated using albumin (ALB) as a reference gene. The results
between the two control genes were totally concordant in 87% of the
cases, and partially concordant in 13% of the cases. For the four
samples that CGH had shown contained alterations in the
.beta..sub.2M locus (15q21.1), ALB was used as the sole reference
gene.
[0232] REL was found to be amplified in virtually all GCB samples
in which high-level 2p14-16 amplifications had been observed by
CGH. The copy number of BCL11A was increased in all but one of
these cases, albeit usually at lower levels than REL. Although CGH
had shown high-level 2p14-16 amplifications in two ABC samples,
RQ-PCR showed merely a gain in REL for these two samples. BCLUA was
amplified in one of these samples and gained in the other. These
results confirm the previous observation that REL may not to the
primary target of amplification in ABC (Rosenwald 2002). CDK4 and
SAS, which map to 12q13-q14, were frequently gained or amplified in
GCB samples that had exhibited 12q gains by CGH, whereas MDM2 was
less commonly altered in these samples. In contrast, all three ABC
sample with 12q13-q14 gains exhibited gains of CDK4, although less
frequently than gains of SAS or MDM2. RPC4 and BCL6, located in
3q27, were gained or amplified in all ABC and GCB samples in which
3q27-qter gains or amplifications had been observed by CGH. MALT1
and BCL2 were commonly gained or amplified in ABC and GCB samples
that had exhibited 18q21 gains, by CGH, while MADH4 was less
frequently altered.
[0233] To determine the influence of these chromosomal alterations,
on locus-specific gene expression, mRNA levels of genes located in
four recurrently gained/amplified regions (2p14-p16, 3q27-qter,
12q12-q15, and 18q21-q22) were correlated with copy number changes.
It was found that each of these chromosomal alterations was
associated with a higher expression levels for a subset of genes
within the region, but these genes differed between DLBCL
subgroups.
[0234] 14 genes were mapped to the chromosomal region 2p14-p16. GCB
and ABC samples with increased genomic copy numbers in this region
showed significant overexpression of 8 (57%) and 5 (36%) of these
14 genes, respectively (FIGS. 30A and 30B). Four of the genes
(VRK2, XPO1, SLC14A, and ACTR2) were significantly overexpressed in
both GCB and ABC samples (FIGS. 30A and 2B). In contrast, REL,
ASHA2, MDH1, and UGP2 were only overexpressed in GCB-DLBCL with
2p14-p16 gains (FIG. 30A),
[0235] GCB and ABC samples with gains/amplifications in the
12q12-q15 region showed significant overexpression of 10 (19%) and
12 (23%) of the >52 genes represented on the Lymphochip
microarray. Five of these genes were overexpressed in both GCB and
ABC samples (SENP1, MCRS1, MARS, SAS, and CDK4) (FIG. 30F). Most of
the overexpressed genes clustered to the chromosomal region
12q13.
[0236] 7 (33%) of the 21 genes mapping to chromosome 3q27-qter were
significantly overexpressed in ABC (FIG. 30C), versus only 2 (13%)
in GCB. Similarly, 9 (75%) of the 12 genes mapping to chromosome
18q21-q22 were significantly overexpressed in ABC (FIG. 30E),
versus only 4 (33%) in GCB (FIG. 30D). All 4 18q21-q22 genes
overexpressed in GCB (MADH2, MADH4, LOC51320, and PMAIP1) were also
overexpressed in ABC.
[0237] To determine whether the various genetic alterations
identified in DLBCL samples influence previously defined gene
expression signatures, gene expression signature averages were
created for each DLBCL, and then evaluated within tumors with
specific chromosomal alterations (Bea 2005). Statistically
significant associations were observed between several chromosomal
alterations and the proliferation, lymph node, T-cell, and MHC
class II gene expression signatures. In particular, gains of
various cytobands of chromosome 3 and losses in 6q21 were both
associated with increased expression of the proliferation gene
expression signature (FIG. 31). Copy number gains of the
chromosomal regions 3p12 and 3q12 were associated with decreased
expression of the MHC class II gene expression signature. Genetic
losses of 6q21 and other cytobands of chromosome 6, as well as
losses of 17p13, gains of Xp11, gains of 11q24-q25, gains of 12q12,
and gains of several cytobands in 7p and 7q all decreased
expression of the T-cell gene expression signature. Finally, gains
of Xp21 were associated with increased expression of the lymph node
gene expression signature, while gains of 3q22 or several
additional cytobands in 3p and 3q were associated with decreased
expression of lymph node gene expression signature.
[0238] The prognostic value of each DLBCL chromosomal alteration
was analyzed across all DLBCL samples and within each DLBCL subtype
separately. Although several chromosomal alterations were
individually associated with a significant increase or decrease in
overall survival rate, only gains within certain regions of
chromosome 3 were significantly associated with shorter overall
survival after adjustment for multiple comparisons in the whole
series of patients. These regions were 3p11-p12, 3q11-q13,
3q21-q24, and 3q25-q27.
[0239] Previously, a gene expression-based DLBCL survival predictor
had been developed using four gene expression signatures and BMP6
(Rosenwald 2002). This survival predictor had the following
formula;
Survival predictor score=[0.241*(proliferation gene expression
signature value)]+[0.310*(BMP6)]-[0.290*(germinal center B cell
gene expression signature value)]-[0.311*(MHC class II gene
expression signature value)]-[0.249*(lymph node gene expression
signature value)].
[0240] This model could divide DLBCL patients into four quartile
groups with 5-year survival rates of 73%, 71%, 34%, and 15%. To
determine whether the chromosome 3 gains discussed above could
improve this survival predictor, a multivariate analysis was
performed. In this analysis, chromosome 3 gains involving the
3p11-p12 region had an independent prognostic value and improved
survival predictions obtained using gene expression data alone
(FIG. 32). Cases with gains of 3p11-p12 were primarily, those that
had been categorized in the least favorable quartile survival group
using gene expression data alone. However, several cases with
3p11-p12 gains had been included in the more favorable quartile
survival groups based on gene expression data. These cases had a
significantly worse clinical prognosis than would have been
predicted by gene expression data alone.
Example 10
Development of an MCL Survival Predictor Using Gene Expression Data
From Affymetrix U133A and U133B Microarrays
[0241] The connection between higher expression of proliferation
genes and worse survival in MCL had previously been documented and
validated (Rosenvvald 2003a). A cluster of proliferation genes had
been identified in the DLBCL samples used to create the DLBCL
survival predictor described in Example 7. By averaging the
expression of these genes, a proliferation gene expression
signature value had been developed for the DLBCL samples. The
correlation of this signature with each probe set on the U133A and
U133B microarrays was determined, and the 22 genes for which the
correlation was greater than 0.5 were labeled proliferation genes.
The correlation between expression of these proliferation genes and
survival in 21 MCL samples was estimated using the Cox proportional
hazards model. Table 2377 lists these 21 MCL samples.
TABLE-US-00022 TABLE 2377 Length of follow-up Status at Used in
creating Sample ID # (years) follow-up survival predictor? MCL_1012
3.19 Alive Yes MCL_1091 3.03 Alive Yes MCL_1114 0.59 Dead Yes
MCL_1128 0.43 Dead Yes MCL_1150 3.21 Dead Yes MCL_1162 0.78 Alive
Yes MCL_1166 0.53 Dead Yes MCL_1194 0.55 Alive Yes MCL_885 1.19
Alive Yes MCL_918 1.95 Dead Yes MCL_924 5.48 Dead Yes MCL_925 7.23
Alive Yes MCL_926 5.18 Dead Yes MCL_936 2.80 Alive Yes MCL_939 1.07
Dead Yes MCL_953 2.31 Dead Yes MCL_956 1.40 Dead Yes MCL_964 0.75
Alive Yes MCL_966 0.21 Dead Yes MCL_968 1.59 Dead Yes MCL_970 5.02
Dead Yes
Out of the 22 proliferation genes, 11 were significant at a 0.001
level. The expression level of these 11 genes in each of the 21 MCL
samples was averaged to generate a proliferation gene expression
signature value. No other genes represented on the U133A or U133B
microarrays correlated with MCL survival to an extent greater than
would be expected by chance, so the final model included only
proliferation genes. The 11 genes used to generate the model are
presented in Table 2378.
TABLE-US-00023 TABLE 2378 Signature UNIQID Gene Symbol
Proliferation 1097290 CIRH1A Proliferation 1101295 FLJ40629
Proliferation 1119729 TK1 Proliferation 1120153 LMNB1 Proliferation
1120494 CDC6 Proliferation 1124745 KIAA0056 Proliferation 1126148
DKFZp586E1120 Proliferation 1130618 TPI1 Proliferation 1134753
WHSC1 Proliferation 1139654 ECT2 Proliferation 1140632 IMAGE:
52707
[0242] A survival predictor score for MCL was generated using the
following equation:
Survival predictor score=1.66*(proliferation gene expression
signature value).
This model was associated with survival in a statistically
significant manner (p=0.00018). To illustrate the significance of
the model in predicting survival, the 21 MCL samples were divided
into two equivalent groups based on their survival predictor
scores. Those samples with survival predictor scores above the
median were placed in the high proliferation group, while those
with survival predictor scores below the median were placed in the
low proliferation group. FIG. 13 illustrates the Kaplan Meier
survival estimates for these;two groups. Median survival for the
high proliferation group was 1.07 years, while median survival for
the low proliferation group was 5.18 years.
Example 11
Development of an MCL Survival Predictor Using Gene Expression Data
From the Lymph Dx Microarray
[0243] A set of 21 genes associated with proliferation and poor
prognosis in MCL had been identified previously (Rosenwald 2003a).
Of these 21 genes, only four were represented on the Lymph Dx
microarray. In order to find a larger set of genes on the Lymph Dx
microarray associated With survival in MCL, Lymphochip expression
data (Rosenwald 2003a) was re-analyzed and another set of
proliferation genes whose expression levels were correlated with
poor survival in MCL were identified. Thirteen of these genes were
represented on the Lymph Dx microarray (median expression >6 on
log.sub.2 scale). These 13 genes are listed in Table 2379.
TABLE-US-00024 TABLE 2379 Unigene ID Build 167 Signature UNIQID
http://www.ncbi.nlm.nih.gov/UniGene Gene symbol Proliferation
1119294 156346 TOP2A Proliferation 1119729 164457 TK1 Proliferation
1120153 89497 LMNB1 Proliferation 1121276 24529 CHEK1 Proliferation
1123358 442658 AURKB Proliferation 1124178 446579 HSPCA
Proliferation 1124563 249441 WEE1 Proliferation 1130799 233952
PSMA7 Proliferation 1131274 374378 CKS1B Proliferation 1131778
396393 UBE2S Proliferation 1132449 250822 STK6 Proliferation
1135229 367676 DUT Proliferation 1136585 80976 MKI67
[0244] The expression levels of the 13 genes listed in Table 2379
on the Lymph Dx microarray were transformed into the log.sub.2
scale and averaged to form a proliferation gene expression
signature value. This was used to generate a survival predictor
score using the following equation:
Survival predictor score=1.66*(proliferation gene expression
signature value).
[0245] For the 21 MCL samples analyzed, the survival predictor
score had a mean of 14.85 and a standard deviation of 1.13, Even in
this limited sample set, the survival predictor score was
significantly associated with prognosis (p=0.0049), with each unit
increase in the score corresponding to a 2.7 fold increase in the
relative risk of death. Data for all 21 samples is shown in Table
2380.
TABLE-US-00025 TABLE 2380 Proliferation Survival Sample ID #
signature value predictor score MCL_1012 8.83 14.658 MCL_1091 8.81
14.625 MCL_1114 10.39 17.247 MCL_1128 10.12 16.799 MCL_1150 8.33
13.828 MCL_1162 8.15 13.529 MCL_1166 9.40 15.604 MCL_1194 7.44
12.350 MCL_885 8.68 14.409 MCL_918 9.33 15.488 MCL_924 8.35 13.861
MCL_925 8.86 14.708 MCL_926 8.14 13.512 MCL_936 8.56 14.21 MCL_939
9.14 15.172 MCL_953 9.25 15.355 MCL_956 9.35 15.521 MCL_964 9.74
16.168 MCL_966 8.76 14.542 MCL_968 9.10 15.106 MCL_970 9.27
15.388
[0246] To illustrate the significance of the model in predicting
survival, the 21 MCL samples were divided into two equivalent
groups based on their survival predictor scores. Those samples with
survival predictor scores above the median were placed in the high
proliferation group, while those with survival predictor scores
below the median were placed in the low proliferation group. FIG.
14 illustrates the Kaplan Meier survival estimates for these two
groups.
Example 12
Identification of Lymphoma Samples as MCL Based on Bayesian
Analysis of Gene Expression Data From Affymetrix U133A and U133B
Microarrays
[0247] A statistical method based on Bayesian analysis was
developed to distinguish MCL samples from samples belonging to
other lymphoma types based on gene expression profiling. This
method was developed using the gene expression data obtained in
Example 1 for the following lymphoma types: ABC, GCB, PMBL, BL, FH,
FL, MALT, MCL, PTLD, SLL, and splenic marginal zone lymphoma
(splenic). Tables 1707-1741 (discussed in Example 1) provide gene
expression data for samples within each of these lymphoma types.
Including the expression level of each gene and the difference in
expression of each gene between types. Tables 1710, 1715, and 1723
(corresponding to FL, MCL, and DLBCL, respectively) include the
correlation between expression of each gene and survival.
[0248] To determine the lymphoma type of a sample, a series of
predictor models are generated. Each predictor model calculates the
probability that the sample belongs to a first lymphoma type rather
than a second lymphoma type. A method was developed to determine
whether a sample was MCL, or one of the following lymphoma types:
ABC, BL, FH, FL, GCB, MALT, PMBL, PTLD, SLL, or splenic. This
method required ten different predictor models, each designed to
determine whether the sample belonged to MCL or one of the other
ten lymphoma types (e.g., MCL vs. ABC, MCL vs. BL, etc.),
[0249] Several of the lymphoma samples analyzed displayed a
tendency towards elevated or reduced expression of genes from the
lymph node and proliferation gene expression signatures. These
genes are likely to be highly differentially expressed between the
lymphoma types, but they do not serve as good predictor genes
because they are often variably expressed within a single lymphoma
type. For this reason, any gene that displayed a correlation with
the proliferation or lymph node signatures was eliminated from
consideration.
[0250] For each lymphoma type pair (e.g., MCL vs. ABC, MCL vs. FL,
etc.), 20 genes were identified that exhibited the greatest
difference in expression between MCL and the second lymphoma type
according to a Student's t-test. The choice to use 20 genes was
arbitrary. For each sample X, the 20 genes were used to generate a
linear predictor score (LPS) according to the following
formula:
LPS ( X ) = j = 1 20 t j X j , ##EQU00003##
where X.sub.j is the expression of gene j in sample X and t.sub.j
is the t-statistic for the difference in expression of gene/between
a first lymphoma type and a second lymphoma type. This is merely
one method for generating an LPS. Others methods include linear
discriminant analysis (Dudolt 2002), support vector machines (Furey
2000), or shrunken centroids (Tibshirani 2002). In addition, there
is no requirement that a t-statistic be used as the scaling
factor.
[0251] After an LPS had been formulated for each lymphoma sample,
the mean and standard deviation of these LPS's was calculated for
each lymphoma type. For a new sample X, Bayes' rule can be used to
estimate the probability that the sample belongs to a first
lymphoma type rather than a second lymphoma type (FIG. 16). In this
example, Bayes' rule was used to calculate the probability q that
sample X was MCL rather than a second lymphoma type using the
following equation:
q ( X is type 1 ) = .phi. ( LPS ( X ) ; .mu. ^ 1 , .sigma. ^ 1 )
.phi. ( LPS ( X ) ; .mu. ^ 1 , .sigma. ^ 1 ) + .phi. ( LPS ( X ) ;
.mu. ^ 2 , .sigma. ^ 2 ) ##EQU00004##
where type 1 is MCL, type 2 is one of the other nine lymphoma
types, .phi.(x; .mu., .sigma.) is the normal density function with
mean .mu. and standard deviation .sigma., {circumflex over
(.mu.)}.sub.1 and {circumflex over (.sigma.)}.sub.1 are the sample
mean and variance of the LPS values for lymphoma type 1, and
{circumflex over (.mu.)}.sub.2 and {circumflex over
(.sigma.)}.sub.2 are the sample mean and variance of the LPS values
for lymphoma type 2.
[0252] This method was used to develop ten predictor models, one
for each pairing of MCL and a second lymphoma type. A sample was
classified as MCL if each of the ten predictors generated at least
a 90% probability that the sample was MCL. If any of the ten
predictors indicated a probability of less than 90% the sample was
classified as non-MCL.
[0253] The 10 sets of 20 genes that were included in these models
and the t-statistics for each gene are presented in Tables
2381-2490.
TABLE-US-00026 TABLE 2381 MCL vs. ABC predictor genes UNIQID Gene
name Scale Factor 1103711 Homo sapiens cDNA FLJ11833 fis, clone
HEMBA1006579. 17.88496416 1133111 PDE9A -- phosphodiesterase 9A
17.61579873 1137987 PLXNB1 -- plexin B1 17.47030156 1132835 SOX11
-- SRY (sex determining region Y)-box 11 16.89404131 1109505 Homo
sapiens, Similar to LOC168058, clone MGC: 39372 15.78111902 IMAGE:
5089466, mRNA, complete cds 1139054 LOC58486 -- transposon-derived
Buster1 transposase-like 15.77800815 protein 1119361 TIA1 -- TIA1
cytotoxic granule-associated RNA binding 15.68070962 protein
1115226 KIAA1683 -- KIAA1683 protein 15.67954057 1101211 Homo
sapiens cDNA: FLJ21960 fis, clone HEP05517. 15.4183527 1118963 Homo
sapiens cDNA FLJ35653 fis, clone SPLEN2013690. 15.36802586 1096503
GL012 -- hypothetical protein GL012 14.64776335 1127849 SNN --
stannin 14.54859775 1099204 Homo sapiens mRNA; cDNA DKFZp586K1922
(from clone 14.32724822 DKFZp586K1922) 1098840 C3orf6 -- chromosome
3 open reading frame 6 14.10346944 1139444 RABL2B -- RAB, member of
RAS oncogene family-like 2B 14.10016196 1106855 KIAA1909 --
KIAA1909 protein 13.9504946 1126695 KIAA0484 -- KIAA0484 protein
13.92285415 1120137 FCGBP -- Fc fragment of IgG binding protein
13.86147896 1133011 TMSNB -- thymosin, beta, identified in
neuroblastoma cells 13.74377784 1133192 GRP3 -- guanine nucleotide
exchange factor for Rap1 -17.09085725
TABLE-US-00027 TABLE 2382 MCL vs. BL predictor genes UNIQID Gene
name Scale Factor 1120900 EPHB6 -- EphB6 13.43582327 1112061 Homo
sapiens cDNA FLJ90513 fis, clone NT2RP3004355. 12.73065392 1109505
Homo sapiens, Similar to LOC168058, clone MGC: 39372 12.63674985
IMAGE: 5089466, mRNA, complete cds 1133099 DNASE1L3 --
deoxyribonuclease I-like 3 12.43333984 1106855 KIAA1909 -- KIAA1909
protein 12.32623489 1110070 ESTs 12.05416064 1121739 ZNF135 -- zinc
finger protein 135 (clone pHZ-17) 11.90460363 1098840 C3orf6 --
chromosome 3 open reading frame 6 11.90309143 1132833 SOX11 -- SRY
(sex determining region Y)-box 11 11.60864812 1121693 KIAA0450 --
KIAA0450 gene product 11.33634052 1123760 ILT7 -- leukocyte
immunoglobulin-like receptor, subfamily A 11.18744726 (without TM
domain), member 4 1125964 KIAA0792 -- KIAA0792 gene product
11.14762675 1112306 ESTs 11.02434114 1096070 DNMT3A -- DNA
(cytosine-5-)-methyltransferase 3 alpha 10.98991879 1129943 Homo
sapiens, similar to Zinc finger protein 85 (Zinc finger 10.72494956
protein HPF4) (HTF1), clone IMAGE: 3352451, mRNA 1118749 PRKWNK1 --
protein kinase, lysine deficient 1 10.64623382 1098954 FLJ13204 --
hypothetical protein FLJ13204 10.46164401 1134749 PRKCBP1 --
protein kinase C binding protein 1 10.40948157 1131860 BIN1 --
bridging integrator 1 10.31084561 1123148 TGFBR2 -- transforming
growth factor, beta receptor II 10.2956213 (70/80 kDa)
TABLE-US-00028 TABLE 2383 MCL vs. FH predictor genes UNIQID Gene
name Scale Factor 1132834 SOX11 -- SRY (sex determining region
Y)-box 11 24.3531072 1100873 ESTs 16.83342764 1109603 ESTs
13.02401995 1139411 OSBPL10 -- oxysterol binding protein-like 10
12.54369577 1106855 KIAA1909 -- KIAA1909 protein 12.10316361
1125193 CNR1 -- cannabinoid receptor 1 (brain) 12.070579 1137450
ALOX5 -- arachidonate 5-lipoxygenase 11.74571823 1100258 KIAA1384
-- KIAA1384 protein 11.60998697 1133167 ZFD25 -- zinc finger
protein (ZFD25) 11.52931491 1136831 PPFIBP2 -- PTPRF interacting
protein, binding protein 2 11.50062692 (liprin beta 2) 1138222 NA
10.99674674 1099437 Homo sapiens mRNA; cDNA DKFZp667B1913 (from
clone 10.90797288 DKFZp667B1913) 1140236 SPAP1 -- SH2 domain
containing phosphatase anchor 10.77082801 protein 1 1114109 DCAL1
-- dendritic cell-associated lectin-1 10.65867119 1098277 PRICKLE1
-- prickle-like 1 (Drosophila) 10.55457068 1135138 CD24 -- CD24
antigen (small cell lung carcinoma cluster 4 10.41999962 antigen)
1103304 Homo sapiens clone CDABP0095 mRNA sequence -10.46625233
1128460 RDGBB -- retinal degeneration B beta -10.91106245 1121953
KIAA0125 -- KIAA0125 gene product -11.22466255 1129281 C14orf110 --
chromosome 14 open reading frame 110 -15.54465448
TABLE-US-00029 TABLE 2384 MCL vs. FL predictor genes UNIQID Gene
name Scale Factor 1132835 SOX11 -- SRY (sex determining region
Y)-box 11 22.14208817 1096070 DNMT3A -- DNA
(cytosine-5-)-methyltransferase 3 alpha 20.53740132 1103711 Homo
sapiens cDNA FLJ11833 fis, clone HEMBA1006579. 20.49880004 1137987
PLXNB1 -- plexin B1 18.38081568 1109505 Homo sapiens, Similar to
LOC168058, clone MGC: 39372 17.17812448 IMAGE: 5089466, mRNA,
complete cds 1098840 C3orf6 -- chromosome 3 open reading frame 6
16.32703666 1130926 C5orf13 -- chromosome 5 open reading frame 13
15.34261878 1096396 SPG3A -- spastic paraplegia 3A (autosomal
dominant) 14.75437736 1132734 COL9A3 -- collagen, type IX, alpha 3
14.684583 1139393 OPN3 -- opsin 3 (encephalopsin, panopsin)
14.39118445 1115537 LOC84518 -- protein related with psoriasis
14.18446144 1102215 Homo sapiens cDNA FLJ11666 fis, clone
HEMBA1004672. 14.16246426 1124585 Homo sapiens cDNA: FLJ21930 fis,
clone HEP04301, -14.33315955 highly similar to HSU90916 Human clone
23815 mRNA sequence. 1137561 HOXA1 -- homeo box A1 -15.38404642
1100581 Homo sapiens mRNA; cDNA DKFZp667A1115 (from clone
-15.91666634 DKFZp667A1115) 1124646 KIAA0084 -- KIAA0084 protein
-16.40577696 1114543 ESTs -17.60167863 1120090 BCL6 -- B-cell
CLL/lymphoma 6 (zinc finger protein 51) -17.63091181 1123731 RGS13
-- regulator of G-protein signalling 13 -22.41602151 1133192 GRP3
-- guanine nucleotide exchange factor for Rap1 -27.28308723
TABLE-US-00030 TABLE 2385 MCL vs. GCB predictor genes UNIQID Gene
name Scale Factor 1098840 C3orf6 -- chromosome 3 open reading frame
6 22.26488562 1132835 SOX11 -- SRY (sex determining region Y)-box
11 17.76179754 1137987 PLXNB1 -- plexin B1 16.86845147 1098954
FLJ13204 -- hypothetical protein FLJ13204 16.65023669 1103711 Homo
sapiens cDNA FLJ11833 fis, clone HEMBA1006579. 15.64719784 1096070
DNMT3A -- DNA (cytosine-5-)-methyltransferase 3 alpha 15.22540494
1139393 OPN3 -- opsin 3 (encephalopsin, panopsin) 14.64030565
1127849 SNN -- stannin 14.28242206 1098156 Human HeLa mRNA isolated
as a false positive in a two- 14.00049272 hybrid-screen. 1128845
FLJ20174 -- hypothetical protein FLJ20174 13.96064416 1129943 Homo
sapiens, similar to Zinc finger protein 85 (Zinc finger 13.85404507
protein HPF4) (HTF1), clone IMAGE: 3352451, mRNA 1140116
DKFZP564B116 -- hypothetical protein DKFZp564B1162 13.81464172
1106855 KIAA1909 -- KIAA1909 protein 13.74521849 1120900 EPHB6 --
EphB6 13.46567004 1127371 Homo sapiens cDNA FLJ14046 fis, clone
HEMBA1006461. 13.45735668 1119361 TIA1 -- TIA1 cytotoxic
granule-associated RNA binding 13.37376559 protein 1120854 EDG1 --
endothelial differentiation, sphingolipid G-protein- 13.1047657
coupled receptor, 1 1098277 PRICKLE1 -- prickle-like 1 (Drosophila)
13.04993076 1140127 TRIM34 -- tripartite motif-containing 34
12.66260609 1100581 Homo sapiens mRNA; cDNA DKFZp667A1115 (from
clone -12.81251689 DKFZp667A1115)
TABLE-US-00031 TABLE 2386 MCL vs. MALT predictor genes UNIQID Gene
name Scale Factor 1132834 SOX11 -- SRY (sex determining region
Y)-box 11 20.7489202 1101987 KIAA1909 -- KIAA1909 protein
10.78991326 1100873 ESTs 10.11845036 1130764 HNRPA0 --
heterogeneous nuclear ribonucleoprotein A0 9.432459453 1102178 Homo
sapiens, Similar to thymosin, beta, identified in 9.035605572
neuroblastoma cells, clone MGC: 39900 IMAGE: 5247537, mRNA,
complete cds 1098277 PRICKLE1 -- prickle-like 1 (Drosophila)
9.003360784 1130926 C5orf13 -- chromosome 5 open reading frame 13
8.712830747 1098694 LOC112868 -- hypothetical protein LOC112868
8.309789856 1103711 Homo sapiens cDNA FLJ11833 fis, clone
HEMBA1006579. 8.248526605 1138099 NA 8.107440225 1120854 EDG1 --
endothelial differentiation, sphingolipid G-protein- 8.045872672
coupled receptor, 1 1102215 Homo sapiens cDNA FLJ11666 fis, clone
HEMBA1004672. 8.032351578 1121739 ZNF135 -- zinc finger protein 135
(clone pHZ-17) 8.020919565 1096070 DNMT3A -- DNA
(cytosine-5-)-methyltransferase 3 alpha 7.964477216 1101211 Homo
sapiens cDNA: FLJ21960 fis, clone HEP05517. 7.738742472 1120825
CHL1 -- cell adhesion molecule with homology to L1CAM 7.516130116
(close homolog of L1) 1099437 Homo sapiens mRNA; cDNA DKFZp667B1913
(from clone 7.209041652 DKFZp667B1913) 1096503 GL012 --
hypothetical protein GL012 7.171540413 1135927 LILRA2 -- leukocyte
immunoglobulin-like receptor, 7.134470829 subfamily A (with TM
domain), member 2 1120645 FADS3 -- fatty acid desaturase 3
7.039952979
TABLE-US-00032 TABLE 2387 MCL vs. PMBL predictor genes UNIQID Gene
name Scale Factor 1132834 SOX11 -- SRY (sex determining region
Y)-box 11 28.17593839 1100873 ESTs 17.90004832 1096503 GL012 --
hypothetical protein GL012 17.43982729 1098840 C3orf6 -- chromosome
3 open reading frame 6 17.37421052 1124734 NA 16.73821457 1135102
PRKCB1 -- protein kinase C, beta 1 16.67436366 1103711 Homo sapiens
cDNA FLJ11833 fis, clone HEMBA1006579. 16.57202026 1140416 TOSO --
regulator of Fas-induced apoptosis 15.64802242 1121757 ADRB2 --
adrenergic, beta-2-, receptor, surface 15.57336633 1140236 SPAP1 --
SH2 domain containing phosphatase anchor 15.20264513 protein 1
1099140 ESTs, Moderately similar to hypothetical protein FLJ20378
15.11929571 [Homo sapiens] [H. sapiens] 1099549 ESTs 14.92883027
1139054 LOC58486 -- transposon-derived Buster1 transposase-like
14.63422275 protein 1138818 ILF3 -- interleukin enhancer binding
factor 3, 90 kDa 14.50621028 1109444 ESTs, Highly similar to
IL24_HUMAN Interleukin-24 14.20430672 precursor (Suppression of
tumorigenicity 16 protein) (Melanoma differentiation associated
protein 7) (MDA-7) [H. sapiens] 1124534 KIAA0553 -- KIAA0553
protein 14.18537487 1098277 PRICKLE1 -- prickle-like 1 (Drosophila)
13.98526258 1131687 TLK1 -- tousled-like kinase 1 13.97468703
1125112 PLCL2 -- phospholipase C-like 2 13.85714318 1125397 Homo
sapiens cDNA FLJ33389 fis, clone BRACE2006871. 13.85049805
TABLE-US-00033 TABLE 2388 MCL vs. PTLD predictor genes UNIQID Gene
name Scale Factor 1109603 ESTs 19.95553782 1138222 NA 15.95397369
1135138 CD24 -- CD24 antigen (small cell lung carcinoma cluster 4
15.89198725 antigen) 1134230 RASGRP2 -- RAS guanyl releasing
protein 2 (calcium and 15.80452978 DAG-regulated) 1139411 OSBPL10
-- oxysterol binding protein-like 10 14.32818885 1140416 TOSO --
regulator of Fas-induced apoptosis 13.89685188 1132834 SOX11 -- SRY
(sex determining region Y)-box 11 13.78424818 1121739 ZNF135 --
zinc finger protein 135 (clone pHZ-17) 13.02195529 1098156 Human
HeLa mRNA isolated as a false positive in a two- 12.95032605
hybrid-screen. 1099270 Homo sapiens cDNA FLJ30555 fis, clone
BRAWH2003818. 12.7877735 1139012 FLJ20373 -- hypothetical protein
FLJ20373 12.70176225 1120654 EDG1 -- endothelial differentiation,
sphingolipid G-protein- 12.25264341 coupled receptor, 1 1120985
KIAA0053 -- KIAA0053 gene product 12.04626201 1115952 LOC146517 --
hypothetical protein LOC146517 11.96299478 1120825 CHL1 -- cell
adhesion molecule with homology to L1CAM 11.82402907 (close homolog
of L1) 1131636 SPOCK2 -- sparc/osteonectin, cwcv and kazal-like
11.80417657 domains proteoglycan (testican) 2 1136706 MYT1 --
myelin transcription factor 1 11.74962191 1113560 Homo sapiens,
clone IMAGE: 5725893, mRNA 11.72049882 1133851 P4HA1 --
procollagen-proline, 2-oxoglutarate 4- -12.59876059 dioxygenase
(proline 4-hydroxylase), alpha polypeptide 1 1137459 BCAT1 --
branched chain aminotransferase 1, cytosolic -14.00465411
TABLE-US-00034 TABLE 2389 MCL vs. SLL predictor genes UNIQID Gene
name Scale Factor 1132834 SOX11 -- SRY (sex determining region
Y)-box 11 23.59602107 1101987 KIAA1909 -- KIAA1909 protein
14.50254794 1103711 Homo sapiens cDNA FLJ11833 fis, clone
HEMBA1006579. 13.31375894 1096070 DNMT3A -- DNA
(cytosine-5-)-methyltransferase 3 alpha 12.37453972 1130926 C5orf13
-- chromosome 5 open reading frame 13 11.27840239 1120845 FADS3 --
fatty acid desaturase 3 11.14057287 1138099 NA 10.92729287 1097887
KIAA0303 -- KIAA0303 protein 10.37913127 1099941 ESTs 10.33953409
1130373 KIAA0303 -- KIAA0303 protein 10.01524528 1110957 SYNE2 --
spectrin repeat containing, nuclear envelope 2 9.865436185 1130320
ESTs 9.807091644 1124373 LPIN1 -- lipin 1 9.024985551 1128813
KREMEN2 -- kringle containing transmembrane protein 2 8.903791941
1131130 MARCKS -- myristoylated alanine-rich protein kinase C
8.688979176 substrate 1120825 CHL1 -- cell adhesion molecule with
homology to L1CAM 8.685132271 (close homolog of L1) 1119752 BASP1
-- brain abundant, membrane attached signal 8.663402838 protein 1
1131854 GCLC -- glutamate-cysteine ligase, catalytic subunit
-8.761521136 1105801 Homo sapiens mRNA; cDNA DKFZp686H1529 (from
clone -8.828675125 DKFZp686H1529) 1097824 MAP2 --
microtubule-associated protein 2 -9.345688564
TABLE-US-00035 TABLE 2390 MCL vs. splenic predictor genes UNIQID
Gene name Scale Factor 1106855 KIAA1909 -- KIAA1909 protein
14.48278638 1121739 ZNF135 -- zinc finger protein 135 (clone
pHZ-17) 11.95918572 1111850 Homo sapiens cDNA FLJ36977 fis, clone
BRACE2006344. 11.13464157 1098024 KIAA1972 -- KIAA1972 protein
10.10869886 1130764 HNRPA0 -- heterogeneous nuclear
ribonucleoprotein A0 10.06898534 1135342 SHOX2 -- short stature
homeobox 2 9.565884385 1097218 MGC45400 -- hypothetical protein
MGC45400 9.187725705 1117193 RINZF -- zinc finger protein RINZF
9.12522795 1139584 PSMD10 -- proteasome (prosome, macropain) 26S
9.066714773 subunit, non-ATPase, 10 1132834 SOX11 -- SRY (sex
determining region Y)-box 11 8.908574745 1131130 MARCKS --
myristoylated alanine-rich protein kinase C 8.732921026 substrate
1131756 PDCD4 -- programmed cell death 4 (neoplastic 8.441424593
transformation inhibitor) 1102187 DKFZp586C102 -- hypothetical
protein DKFZp586C1021 8.391861029 1098195 DKFZp762C111 --
hypothetical protein DKFZp762C1112 8.349839204 1101211 Homo sapiens
cDNA: FLJ21960 fis, clone HEP05517. 8.337208237 1136673 GNAS --
GNAS complex locus 8.254076655 1139116 USP16 -- ubiquitin specific
protease 16 8.179384251 1098694 LOC112868 -- hypothetical protein
LOC112868 7.935903681 1120519 WWP2 -- Nedd-4-like ubiquitin-protein
ligase -7.881202253 1114916 FLJ13993 -- hypothetical protein
FLJ13993 -8.33683119
[0254] With so many candidate predictor genes being utilized, it is
possible to generate a predictor, model that accurately predicts
every element of a training set but fails to perform on an
independent sample. This occurs because the model incorporates and
"learns" the individual characteristics of each sample in the
training set. Leave-one-out cross-validation was used to verify
that the prediction models generated above would work on
independent samples that the models had not encountered previously,
in this cross-validation method, a single sample is removed from
the training set, and the predictor is developed again using the
remaining data. The resulting model is then used to predict the
sample that was removed. This method is repeated with each
individual sample taken out. Since no sample is predicted from a
model that includes that sample, this method provides an unbiased
estimate of predictor accuracy.
[0255] When the predictors developed above were evaluated by
leave-one-out cross-validation. All but one of the 21 MCL samples
were correctly identified as MCL and none of the 489 non-MCL
samples were mistakenly identified as MCL.
Example 13
Identification of Lymphoma Samples as MCL Based on Bayesian
Analysis of Gene Expression Data From a Lymphochip Microarray
[0256] Lymphoma samples with morphology consistent with MCL were
identified by pathological review. Since t(11;14) translocation and
cyclin D1 overexpression have been consistently associated with
MCL, cyclin D1 mRNA levels were measured in each sample by
quantitative RT-PCR. Of the 101 samples analyzed, 92 expressed
cyclin D1 mRNA. These 92 samples, which were deemed the "core
group" of MCLs, were divided into a training set and a validation
set. Gene expression was measured in all 101 samples using a
Lymphochip Microarray (Alizadeh 1999). For comparison, gene
expression was measured in 20 samples identified as SLL. In
addition, MCL expression data was compared to expression data
obtained previously for GCB (134 cases) and ABC (83 cases)
(Rosenwald 2002). Several thousand genes were differentially
expressed between cyclin D1-positive MCL and the other lymphoma
types with high statistical significance (p<0.001). A complete
listing of these genes is available at
http://llmpp.nlh.gov/MCL.
[0257] Three different binary predictor models were developed: MCL
vs. SLL, MCL vs. GCB, and MCL vs. ABC. Each of these models was
designed to calculate the probability that a sample was MCL rather
than the other lymphoma type in the pair. For each pair, the genes
that were most differentially expressed between MCL and the other
lymphoma type in the pair were identified, and the difference in
expression between the lymphoma types was quantified using a
Student's t-test. An LPS was then calculated for each sample using
the following formula:
LPS ( X ) = j = 0 t j X j , ##EQU00005##
where X.sub.j is the expression of gene j in sample X and t.sub.j
is the t-statistic for the difference in expression of gene j
between the two lymphoma types in the pair. Cyclin D1 was excluded
from the calculation of LPS so that the model could be used to
identify potential MCL cases that were cyclin D1 negative.
[0258] After an LPS had been formulated for each lymphoma sample,
the mean and standard deviation of these LPS's was calculated for
each lymphoma type. For a new sample X, Bayes' rule can be used to
estimate the probability q that the sample belongs to MCL rather
than the second lymphoma type in the pair using the following
equation:
q ( X is MCL ) = .phi. ( LPS ( X ) ; .mu. ^ MCL , .sigma. ^ MCL )
.phi. ( LPS ( X ) ; .mu. ^ MCL , .sigma. ^ MCL ) + .phi. ( LPS ( X
) ; .mu. ^ 2 , .sigma. ^ 2 ) ##EQU00006##
where .phi.(x; .mu., .sigma.) is the normal density function with
mean .mu. and standard deviation .sigma., {circumflex over
(.mu.)}.sub.MCL and {circumflex over (.sigma.)}.sub.MCL are the
sample mean and variance of the LPS values for MCL, and {circumflex
over (.mu.)}.sub.2 and {circumflex over (.sigma.)}.sub.2 are the
sample mean and variance of the LPS values for the second lymphoma
type of the pair. A cut-off point of 90% was selected for assigning
a sample to a particular lymphoma type. Every sample in the
training set was classified correctly using this model (FIG. 16).
When applied to the validation set, the model correctly classified
98% of the cyclin D1-positive MCL cases as MCL (FIG. 16).
[0259] This diagnostic test was applied to nine lymphoma cases that
were morphologically consistent with MCL, but negative for cyclin
D1 expression. Seven of these samples were classified as MCL, one
was classified as GCB, and one was not assigned to any lymphoma
type because none of the pairs generated a probability of 90% or
greater
Example 14
Classification of DLBCL Samples Based on Bayesian Analysis of Gene
Expression Data From the Lymphochip Microarray
[0260] A statistical method to classify DLBCL samples based on
Bayesian analysis was developed using gene expression data obtained
using the Lymphochip cDNA microarray (Rosenwald 2002); This data is
available at http://llmpp.nih.gov/DLBCL. The data was divided into
two sets; a training set used to create and optimize the prediction
model, and a validation set to evaluate the performance of the
model. The training set consisted of 42 ABC DLBCL samples and 67
GCB DLBCL samples, while the validation set consisted of 41 ABC
DLBCL samples, 67 GCB DLBCL samples, and 57 type 3 DLBCL samples
(Shipp 2002).
[0261] Genes that were listed as present on >50% of the samples
were identified, and the signal value for these genes on each
microarray was normalized to 1,000. After normalization, all signal
values under 50 were set to 50. A log.sub.2 transformation was then
performed on all the signal values.
[0262] An LPS for distinguishing between two lymphoma types was
calculated for each sample X in the training set using an
equation:
LPS ( X ) = j t j X j , ##EQU00007##
where X.sub.j represents the expression level of gene j and t.sub.j
is a scaling factor whose value depends on the difference in
expression of gene j between the two lymphoma types. The scaling
factor used in this example was the t-statistic generated by a t
test of the difference in gene j expression between two lymphoma
types. Only those genes with the largest t-statistics were included
when calculating the LPS for each sample. The list of genes used to
generate the LPS was narrowed further by including only those genes
that were most variably expressed within the training set. Only
genes in the top third with respect to variance were included.
Genes that displayed a correlation with proliferation or lymph node
signatures (Shaffer 2001; Rosenwald 2002) were eliminated from
consideration, because these genes are often variably expressed
within samples from a single lymphoma type (Rosenwald 2002).
[0263] Since the LPS is a linear combination of gene expression
values, its distribution within each lymphoma type should be
approximately normal, provided that it includes a sufficient number
of genes and the correlation structure of those genes is not
extreme. The mean and variance of these normal distributions within
a lymphoma type can then be estimated from the combined LPS's of
all samples within the type. The LPS distribution of two lymphoma
types can be used to estimate the probability that a new sample
belongs to one of the types using Bayes' rule. The probability q
that a sample Y belongs to lymphoma type 1 can be determined by an
equation:
q ( Y is subtype 1 ) = .phi. ( LPS ( Y ) ; .mu. ^ 1 , .sigma. ^ 1 )
.phi. ( LPS ( Y ) ; .mu. ^ 1 , .sigma. ^ 1 ) + .phi. ( LPS ( Y ) ;
.mu. ^ 2 , .sigma. ^ 2 ) ##EQU00008##
where .phi.(x; .mu., .sigma.) is the normal density function with
mean .mu. and standard deviation .sigma., {circumflex over
(.mu.)}.sub.1 and {circumflex over (.sigma.)}.sub.1 are the sample
mean and variance of the LPS values for lymphoma type 1, and
{circumflex over (.mu.)}.sub.2 and {circumflex over
(.sigma.)}.sub.2 are the sample mean and variance of the LPS values
for lymphoma type 2. This calculation was used to determine the
probability that each sample in the training set belonged to GCB or
ABC. A sample was classified as a particular type if it had a 90%
or greater probability of belonging to that type. The number of
genes in the predictor model was optimized based on the accuracy
with which the predictor classified samples into the ABC or GCB
subtypes defined previously by hierarchical clustering (Rosenwald
2002). The final predictor incorporated 27 genes, and correctly
classified 87% of the training set samples into the subtype to
which they had been assigned by hierarchical clustering (FIG. 17).
The genes included in the predictor are listed in Table 2391.
TABLE-US-00036 TABLE 2391 Unigene ID Build 167 UNIQID
(http://www.ncbi.nlm.nih.gov/UniGene) Gene symbol 19375 235860
FOXP1 19346 109150 SH3BP5 19227 193857 LOC96597 16049 439852 IGHM
32529 55098 C3orf6 24729 127686 IRF4 24899 81170 PIM1 19348 NA NA
27565 444105 ENTPD1 17227 170359 IL16 26919 118722 FUT8 24321
171262 ETV6 29385 167746 BLNK 16858 376071 CCND2 31801 386140 BMF
19234 418004 PTPN1 26385 307734 MME 24361 388737 NA 24570 446198 NA
24904 18166 KIAA0870 24429 155024 BCL6 28224 387222 NEK6 27673
124922 LRMP 24376 317970 SERPINA11 17496 300592 MYBL1 17218 283063
LMO2 28338 78877 ITPKB
[0264] Since the samples used to estimate the distribution of the
LPS's were the same samples used to generate the model, there was a
possibility of overfitting. Overfitting would result in a model
that indicates a larger separation between the LPS's of two
lymphoma types than would be found in independent data. To insure
that overfitting was not taking place, the model was tested on the
validation set. The reproducibility of the predictor model was
verified by its ability to correctly classify 88% of the samples in
the validation set (FIG. 18). Interestingly, 56% of the DLBCL
samples that had been placed in the type 3 subtype by hierarchical
clustering were classified as either ABC or GCB using this Bayesian
model.
[0265] In previous experiments, the genes that were used to
distinguish GCB and ABC were deliberately selected to include those
that were preferentially expressed in normal GCB cells (Alizadeh
2000; Rosenwald 2002). In the present analysis, the predictor model
was not biased a priori to include such genes. The ABC and GCB
lymphoma types as defined by the Bayesian model were analyzed for
differential expression of GCB cell restricted genes. Thirty seven
genes were found to be both more highly expressed in GCB cells than
at other stages of differentiation (p<0.001) and differentially
expressed between DLBCL subtypes (p<0.001) (FIG. 19A). These 37
genes are listed in Table 2392.
TABLE-US-00037 TABLE 2392 Unigene ID Build 167 UNIQID
(http://www.ncbi.nlm.nih.gov/UniGene) Gene symbol 28014 300592
MYBL1 24376 317970 SERPINA11 24429 155024 BCL6 16886 124922 LRMP
27374 283063 LMO2 29912 446198 24510 266175 PAG 24854 439767 TOX
32171 307734 MME 24361 388737 19365 171857 Cyorf15a 27292 272251
KLHL5 24822 283794 PCDHGC3 30923 446195 24825 88556 HDAC1 31696
91139 SLC1A1 26976 434281 PTK2 19279 49614 GCET2 17866 1765 LCK
24386 437459 MYO1E 33013 293130 VNN2 25126 30498 157441 SPI1 26512
379414 MFHAS1 26582 153260 SH3KBP1 17840 132311 MAP2K1 26000 25155
NET1 24323 149342 AICDA 30922 435904 C21orf107 30641 79299 LHFPL2
19308 179608 DHRS9 24455 405387 30034 300208 SEC231P 24977 169939
HS2ST1 24449 206097 RRAS2 30763 446198 27987 73792 CR2
All but two (AICDA and DHRS9) of these 37 genes were more highly
expressed in GCB than in ABC. This demonstrates that the DLBCL
subtypes defined by the Bayesian predictor seem to differ with
respect to their cell of origin, with GCB retaining the gene
expression program of normal GCB cells.
[0266] ABC, on the other hand, displayed higher expression of genes
characteristic of plasma cells (FIG. 19B). Twenty four genes were
found to be both more highly expressed in plasma cells than in B
cells at earlier developmental stages (p<0.001) and
differentially expressed between the DLBCL subtypes (p<0.001).
These 24 genes are listed in Table 2393.
TABLE-US-00038 TABLE 2393 Unigene ID Build 167 UNIQID
(http://www.ncbi.nlm.nih.gov/UniGene) Gene symbol 16614 127686 IRF4
26907 118722 FUT8 31104 313544 NS 19219 355724 CFLAR 26174 28707
SSR3 24566 169948 KCNA3 34500 442808 B4GALT2 26991 314828 UPP1
30191 438695 FKBP11 27402 259855 EEF2K 26096 434937 PPIB 15887 2128
DUSP5 32440 512686 C20orf69 34827 429975 PM5 29232 437638 XBP1
17763 76640 RGC32 32163 445862 RAB30 17814 5353 CASP10 31460 409223
SSR4 26693 83919 GCS1 25130 409563 PACAP 16436 267819 PPP1R2 31610
76901 PDIR 28961 212296 ITGA6
The majority of these plasma cell-restricted genes were more highly
expressed in ABC than in GCB. Eight of the 32 genes encode proteins
that reside and function in the endoplasmic reticulum (ER) or Golgi
apparatus, suggesting that ABCs have increased the intracellular
machinery for protein secretion. These eight genes are denoted in
the above list by the designation "ER" or "goigi" in parentheses.
Another gene on this list, XBP-1 transcription factor, encodes a
protein that is required for plasma cell differentiation (Reimold
2001) and is involved in the response to unfolded proteins in the
ER (Calfon 2002). ABCs have not undergone full plasmacytic
differentiation, however, because other key plasma cell genes such
as Bllmp-1 were not more highly expressed in ABC.
Example 15
Classification of DLBCL Samples Based on Bayesian Analysis of Gene
Expression Data From the Affymetrix HD6860 Microarray
[0267] The prediction method described in Example 14 above was
applied to gene expression data from 58 DLBCL samples obtained
using an Affymetrix HU6800 oligonucleotide microarray (Shipp 2002).
This data is available at www.genome.wi.mit.edu/MPR/lymphoma. The
first step in analyzing this data was to exclude all microarray
features with a median signal value of <200 across the samples.
Multiple microarray features representing the same gene were then
averaged. Of the 27 genes in the DLBCL subtype predictor developed
using the Lymphochip data (above), only 14 were represented on the
Affymetrix array and passed this filtering process. These 14 genes
(are listed in Table 2394.
TABLE-US-00039 TABLE 2394 Unigene ID Build 167 UNIQID
(http://www.ncbi.nlm.nih.gov/UniGene) Gene symbol 24729 127686 IRF4
17227 170359 IL16 26907 118722 FUT8 27565 444105 ENTPD1 16858
376071 CCND2 24899 81170 PIM1 16947 418004 PTPN1 16049 439852 IGHM
26385 307734 MME 27673 124922 LRMP 24429 155024 BCL6 17218 283063
LMO2 28338 78877 ITPKB 17496 300592 MYBL1
These 14 genes were used to create a new DLBCL subtype predictor in
which the LPS scaling coefficients were again calculated based on
the DLBCL subtype distinction in the Lymphochip data set (Rosenwald
2002). To account for systematic measuring differences between the
Affymetrix and Lymphochip microarrays, the expression value of each
gene on the Affymetrix microarray was shifted and scaled to match
the mean and variance of the corresponding expression values on the
Lymphochip. The adjusted expression values for each of the 14 genes
were then used to calculate LPS's for each sample. DLBGL subtype
membership was again assigned on a cut-off of 90% certainty.
Several observations suggested that the predictor identified ABC
and GCB samples within the Affymetrix data set that were comparable
to those found in the Lymphochip data set. First, the relative
proportions of ABC (29%) and GCB (53%) were very similar to the
corresponding proportions in the Lymphochip data set (34% and 49%,
respectively). Second, 43 genes were found to be differentially
expressed between the two DLBCL subtypes with high significance
(p<0.001) in the Affymetrix data. This number is substantially
higher than would be expected by chance, given that the Affymetrix
microarray measures the expression of approximately 5,720 genes.
The symbols for these 43 genes were: IGHM; TCF4; IRF4; CCND2; SLA;
BATF; KIAA0171; PRKCB1; P2RX5; GOT2; SPIB; CSNK1E; PIM2; MARCKS;
PIM1; TPM2; FUT8; CXCR4; SP140; BCL2; PTPN1; KIAA0084; HLA-DMB;
ACP1; HLA-DQA1; RTVP1; VCL; RPL21; ITPKB; SLAM; KRT8; DCK; PLEK;
SCA1; PSIP2; FAM3C; GPR18; HMG14; CSTB; SPINK2; LRMP; MYBL1; and
LMO2. Third, the 43 genes differentially expressed between the
types included 22 genes that were not used in the predictor but
were represented on Lymphochip arrays. Fourteen of these 22 genes
were differentially expressed on the Lymphochip array with high
statistical significance (p<0.001). Finally, the expression of
the c-rel gene was previously found to correspond to amplification
of the c-rel genomic locus in DLBCL tumor cells, and oncogenic
event occurring in GCB but not ABC (Rosenwald 2002). In the
Affymetrix data set, c-rel was differentially expressed between the
two subtypes (p=0.0025), and was highly expressed only in a subset
of GCB's.
Example 16
Identification of DLBCL Samples as PMBL Based on Bayesian Analysis
of Gene Expression Data From the Lymphochip Microarray
[0268] 310 lymphoma biopsy samples identified as DLBCL by a panel
of hematopathologists were divided into a 36 sample training set
and a 274 sample validation set, with the validation set consisting
of the DLBCL samples classified previously in Example 14. All
patients from whom the sample's were derived had been treated with
anthracycline-containing multiagent chemotherapy protocals, with
some patients additionally receiving radiation therapy. The
training set was profiled for gene expression using Lymphochip
microarrays comprising 15,133 cDNA elements as described previously
(Alizadeh 2000). This data is available at
http://llmpp.nih.gov/PMBL. The validation set had previously been
profiled using Lymphochip microarrays comprising 12,196 cDNA
elements (Rosenwald 2002). This data is available at
http;//llmpp.nih.gov/DLBCL.
[0269] A hierarchical clustering algorithm (Elsen 1998) was used to
organize the genes by their expression patterns across the 36
samples in the training set. A large group of genes that were more
highly expressed in lymphomas with mediastinal involvement than in
other DLBCLs was shown to be tightly clustered in the resulting
dendrogram (FIG. 20A). This cluster of genes included two genes,
MAL and FIG1, previously shown to be highly expressed in PMBL
(Copie-Bergman 2002; Copie-Bergman 2003). Several of the lymphomas
with mediastinal involvement did not express this set of putative
PMBL signature genes, and it was, suspected that these samples were
more likely to be conventional DLBCL than PMBL. Hierarchical
clustering was used to organize the samples according to their
expression of the PMBL signature genes, resulting in two major
clusters of cases (FIG. 20B). One cluster contained 21 samples
designated PBML core" samples by virtue of their higher expression
of PMBL signature genes. The other cluster contained some samples
that had virtually no expression of these genes, and other samples
that did express these genes but at lower levels than the PMBL core
samples.
[0270] A gene expression-based method for distinguishing PMBL core
cases from GCB and ABC DLBCL cases based on Bayesian analysis was
developed using the methods described in Examples 14 and 15, A set
of genes were selected that were differentially expressed between
the PMBL core samples and both GCB and ABC (p<0.001). This set
of genes included all of the PMBL signature genes identified by
hierarchical clustering (FIG. 20A), as well as a large number of
additional genes. Many of the genes in this set belonged to the
lymph node gene expression signature (Alizadeh 2000; Rosenwald
2002). These genes were excluded from the final predictor because
they might cause some DLBCL samples with higher expression of lymph
node gene expression signature genes to be misclassified as PMBL.
The list of PMBL distinction genes was refined by adding a
requirement that they also be differentially expressed between the
PMBL core samples and a subgroup of six DLBCL samples with higher
expression of lymph node gene expression signature genes
(p<0.001). The resulting set of 46 genes included 35 genes that
were more highly expressed in PMBL and 11 genes that were more
highly expressed in DLBCL (FIG. 21A). The 46 genes in this set were
PDL2, SNFT, IL13RA1, FGFR1, FLJ10420, CCL17/TARC, TNFRSF8/CD30,
E2F2, MAL, TNFSF4/OX40 ligand, IL411/Fig1, IMAGE:686580, BST2,
FLJ31131, FCER2/CD23, SAMSN1, JAK2, FLJ00066, MST1R, TRAF1, SLAM,
LV75, TNFRSF6/Fas, FNBP1, TLR7, TNFRSF17/BCMA, CDKN1A/p21CIP1,
RGS9, IMAGE:1340506, NFKB2, KIAA0339, ITGAM, IL23A, SPINT2, MEF2A,
PFDN6, ZNF141, IMAGE:4154313, IMAGE:825382, DLEU1, ITGAE, SH3BP5,
BANK, TCL1A, PRKAR1B, and CARD11. A series of linear predictor
scores were generated based on the expression of this gene set.
Based on the distribution of linear predictor scores within; a
particular lymphoma type, Bayes' rule can be used to estimate the
probability that a particular sample belongs to either of the two
types. An arbitrary probability cut-off of 90% or greater was used
to classify a sample as a particular lymphoma type. All of the PMBL
core samples were classified as PMBL using this method, as were six
of the other lymphoma samples with mediastinal involvement.
However, nine of the lymphoma samples with mediastinal involvement
were classified as a DLBCL, as were all of the GCB and ABC
samples.
[0271] In the validation set, 11 samples were identified on
clinical grounds as being consistent with a diagnosis of PMBL, and
the Bayesian model classified nine of these as PMBL (FIG. 21B).
Interestingly, 12 of the remaining 263 DLBCL samples were
classified as PMBL by the predictor. FIG. 21B shows that these
cases were indistinguishable by gene expression from the nine cases
diagnosed as PMBL on clinical grounds. As expected, the average
expression of the PMBL predictor genes in the 249 samples
classified as DLBCL was notably lower than in the 22 PMBL cases.
Thus, PMBL represents a third subgroup of DLBCL than can be
distinguished from ABC and GCB by gene expression profiling.
[0272] Table 2395 compares the clinical parameters of patients
assigned to the PMBL, ABC, and GCB subgroups of DLBCL using this
prediction method.
TABLE-US-00040 TABLE 2395 ABC GCB PMBL PMBL PMBL DLBCL DLBCL
Training set Validation set All cases P value Median age 66 61 33
33 33 4.4E-16 Age <35 5% 10% 52% 56% 53% 7.2E-14 Age 35-60 29%
38% 44% 28% 37% Age >60 66% 52% 4% 17% 9% Gender = male 59% 53%
44% 50% 47% 0.38 Female <35 2% 3% 32% 39% 35% 1.1E-12 Male
<35 2% 7% 20% 17% 19% Female 35-60 6% 18% 24% 6% 16% Male 35-60
23% 19% 20% 22% 21% Female >60 33% 25% 0% 6% 2% Male >60 34%
27% 4% 11% 7%
PMBL patients were significantly younger than other DLBCL patients,
with a median age at diagnosis of 33 years compared with a median
age of 66 and 61 years for ABC and GCB patients, respectively.
Although there was no significant difference in gender distribution
among the DLBCL subgroups, young women (<35 years) accounted for
35% of PMBL patients, more than any other DLBCL subgroup. Young men
(<35 years) were also more frequently represented in the PMBL
subgroup, accounting for 19% of the patients. Correspondingly,
older men and women (age>60) were significantly underrepresented
in the PMBL subgroup. These clinical characteristics were observed
in both the training set and the validation set of PMBL cases,
demonstrating that the PMBL predictor reproducibly identified a
clinically distinct subgroup of DLBCL patients.
[0273] The PMBL subgroup defined by the PMBL predictor had a
relatively favorable overall survival rate after therapy (FIG. 22).
PMBL patients had a five-year survival rate of 84%, superior to the
46% rate seen in DLBCL patients as a whole (p=0.0067). The survival
of the PMBL subgroup was significantly better than the 30%
five-year survival rate of the ABC subgroup (FIG. 22; p=5.8E-5),
but only marginally better than the 59% five-year survival rate of
the "GCB subgroup (p=0.18).
Example 17
Classification of Lymphomas Into Types Based on Bayesian Analysis
of Gene Expression Data From the Lymph Dx Microarray
[0274] Based on the clustering of the Lymph Dx microarray signals
for the DLBCL samples, a cluster of "proliferation signature" genes
and a cluster of "lymph node signature" genes were identified, the
expression of these genes was averaged to form a proliferation
signature and a lymph node signature. Each gene represented on the
Lymph Dx microarray was placed into one of three "gene-list
categories" based on its correlation with the proliferation or
lymph node gene signatures. "Proliferation" genes were defined as
those genes for which the correlation between their expression and
the proliferation signature was greater than 0.35. Lymph node genes
were defined as those genes for which the correlation between their
expression and the lymph node signature was greater than 0.35. The
remaining genes on the array were classified as standard genes.
This classification resulted in 323 proliferation genes and 375
lymph node genes.
[0275] Two stages of lymphoma classification were performed using
the gene expression data obtained for the above samples using the
Lymph Dx microarray. The general procedure used to classify the
samples is presented in flow chart form in FIG. 1.
[0276] For the first stage of expression analysis, the samples were
divided into five types: FL, MCL, SLL, FH, and a class of
aggressive lymphomas that included DLBCL and BL. Samples obtained
from subjects with other diagnoses (e.g., MALT, LPC) were omitted
from this analysis. Data from the Lymph Dx microarray was then used
to compare gene expression in each possible lymphoma type pair
(e.g., FH vs. FL, MCL vs. SLL, etc.). This resulted in the creation
of ten "pair-wise models" (one for each possible lymphoma type
pair) for predicting whether a sample fell into a particular
lymphoma type.
[0277] For each lymphoma type pair, the difference in expression
between the two; types for every gene on the microarray was
calculated, and a t-statistic was generated to represent this
difference. Within each gene-list category (proliferation, lymph
node, and standard), individual genes were ordered based on the
absolute value of their t-statistic. Only those genes that
displayed a statistically significant difference in expression
between the two types were included in the model. Those genes with
largest absolute t-statistics in each gene-list category were then
used to generate a linear predictor score (LPS) for each sample.
For a sample X and a set of genes G, the LPS was defined as:
LPS ( X ) = j = 0 t j X j , ##EQU00009##
where X.sub.j is the expression of gene j in the sample and t.sub.j
is the t-statistic representing the difference in expression of
gene j between the two lymphoma types. This formulation of LPS,
known as the compound coagulate predictor, has previously been used
successfully (Radmacher 2002; Rosenwald 2003a; Wright 2003). Other
ways to formulate an LPS include Fisher linear discriminant
analysis (Dudolt 2002), weighted voting (Golub 1999), linear
support vector machines (Ramaswamy 2001), and nearest shrunken
centroids (Tibshirani 2002).
[0278] In order to optimize the number of genes used to generate
the LPS, a series of LPS's were generated for each sample using
between five and 100 genes from each gene-list category. The
optimal number of genes is that number which generates a maximum
t-statistic when comparing the LPS of two samples from different
lymphoma types (FIG. 23). This optimization procedure was repeated
for every geno-list category in every pair-wise model, meaning that
30 optimizations were performed in all.
[0279] It was recognized that for some pair-wise models, it would
be useful to calculate LPS's using different combinations of
gene-list categories. LPS's were calculated for each sample using
four different combinations. In the first, LPS was calculated using
the standard genes only. In the second, LPS's were calculated for
both the standard and proliferation genes, but not the lymph node
genes. In the third, LPS's were calculated for both the standard
and lymph node genes, but not the proliferation genes. In the
fourth, LPS's were calculated using all three gene-list
categories.
[0280] Depending on the number of gene-list categories included,
between one and three LPS's were calculated for each sample in the
pair-wise models. Thus, each sample could be thought of as a vector
in a space of between one and three dimensions. Since the LPS's
were sums of individual expressions, it was reasonable to
approximate the distributions as normal. Multivariate normal
distributions are defined by two,quantities: a mean vector, which
indicates the average value of each of the models within a given
lymphoma type, and a covariance matrix, which indicates the
magnitude and orientation spread of points away from this center.
Both of these quantities can be estimated empirically from the
observed data. FIG. 24 shows the Standard and Proliferation LPS's
for the FL vs. DLBCL/BL pair-wise model. The dotted lines indicate
the standard deviations from the fitted multivariate normal
distributions.
[0281] Once the multidimensional distributions have been estimated,
Bayes' rule. (Bayes 1763) can be used to estimate the probability
that a given sample belongs to one lymphoma type or another.
Bayesian analysis of an LPS has been successfully employed in the
past to distinguish DLBCL subtypes (Rosenwald 2003a, Wright 2003).
For a sample X, the probability q of the sample belonging to a
first lymphoma type rather than a second lymphoma type can be
calculated using the formula:
q = .phi. ( LPS ( X ) ; .mu. ^ 1 , .sigma. ^ 1 ) .phi. ( LPS ( X )
; .mu. ^ 1 , .sigma. ^ 1 ) + .phi. ( LPS ( X ) ; .mu. ^ 2 , .sigma.
^ 2 ) ##EQU00010##
where LPS(X) is the linear predictor score for sample X, .phi.(x,
.mu., .sigma.) is the normal density function with mean .mu. and
standard deviation .sigma., {circumflex over (.mu.)}.sub.1 and
{circumflex over (.sigma.)}.sub.1 are the mean and variance of the
LPS's for the first lymphoma type, and {circumflex over
(.mu.)}.sub.2 and {circumflex over (.sigma.)}.sub.2 are the mean
and variance of the LPS's for the second lymphoma type. Using this
equation, a single probability q value can be developed for each
sample and for each of the four LPS combinations. This q value can
then be used to classify a sample as a first lymphoma type, a
second lymphoma type, or unclassified. Samples with the highest q
values are classified as the first lymphoma type, while samples
with the lowest q values are classified as the second lymphoma
type. Samples with middle range q values are deemed unclassified.
Classifying the samples in this manner requires two cut-off points:
a lower cut-off point between the second lymphoma type and
unclassified, and an upper cut-off point between unclassified and
the first lymphoma type. To develop these cut-off points, samples
were ordered by their q values, band each possible cut-off point
between adjacent samples was considered. To ensure that the cut-off
points were reasonable, the lower cut-off point was restricted to
between 0.01 and 0.5 and the upper cut-off point was restricted to
between 0.5 and 0.99.
[0282] Every cut-off point and model combination was analyzed by
the following equation:
3.99*[(% of type 1 misidentified as type 2)+(% of type 2
misidentified as type 1)]+[(% of type 1 unclassified)+(% of type 2
misidentified)].
Using this equation, the cut-off point would be adjusted to allow
an additional error only if this adjustment resulted in four or
more unclassified samples becoming correctly classified. The final
model and cut-off point for a given pair-wise analysis was that
which minimized this equation. The equation utilizes percentages
rather than the actual number of cases in order to account for the
different number of samples in each class.
[0283] All cut-off points between a given pair of adjacent g-values
will produce the same division of data. Since cut-off point
optimality is defined in terms of dividing the data into subtypes,
all cut-off points between a pair of borderline cases wilt be
equally optimal, in choosing where to place the actual cut-off
point values, values were chosen that would lead to a larger
unclassified region. When the lower cut-off point was being
defined, a value would be chosen that was 1/5 of the way from the
smallest borderline case to the largest. When the upper cut-off
point was being defined, a value would be chosen that was 4/5 of
the way from the smallest borderline case to the largest. FIG. 25
illustrates the q-results of optimizing the cut-point for the FL
versus DLBCL/BL samples. The optimal lower cut-off point for these
samples was found at q=0.49, while the optimal upper cut-off point
was found at q=0.84. FIG. 26 indicates; how this choice of cut-off
points divided the space of LPS's.
[0284] The above procedures resulted in a series of pair-wise
models for comparing every lymphoma type to every other lymphoma
type. If there are n types, then there will be n-1 pair-wise models
for each type. Since there were five lymphoma types in the stage 1
analysis, each type was involved in 4 pair-wise models. For
instance, there were four different pair-wise models for MCL; MCL
vs. FH, MCL vs. FL, MCL vs. SLL, and MCL vs. DLBCL/BL. For each
sample tested, each pair-wise model will produce one of three
possible results: 1) the sample belongs to the first lymphoma type
of the pair-wise model, 2) the sample belongs to the second
lymphoma type of the pair-wise model, or 3) the sample is
unclassified. If each of the n-1 models agrees that the sample
belongs to a particular lymphoma type, then the sample is
designated as belonging to that type. If the n-1 models do not all
agree that the sample belongs to a particular lymphoma type, the
sample is designated as unclassified.
[0285] To ensure that the above methods did not result in
overfitting (i.e., models that fit particular idiosyncrasies of the
training set but fall when applied to independent data), the models
were validated by leave-one-out cross-validation fashion (Hills
1966). Each sample was removed from the data one at a time, and a
predictive model was developed as described above using the
remaining data. This model was then used to predict the sample that
was removed. Since the model being used to predict a given sample
was generated from data that did not include that sample, this
method provided an unbiased estimate of the accuracy of the
model.
[0286] The results of the leave-one-out predictions are set forth
in Tables 2396 and 2397, below. The rows in each table correspond
to different sample groups, while the columns indicate the
prediction results. The standard to which the prediction results
were compared in this stage was the diagnoses of a panel of eight
expert hematopathologists who used histological morphology and
immunohistochemistry to classify the samples. Table 2396 provides
classification results for the five lymphoma types tested
(DLBCL/BL, FL, FH, MCL, SLL), while Table 2397 provides more
specific results for classification of subtypes within these five
lymphoma types. The results set forth in Table 2396 are also
summarized in FIG. 27.
TABLE-US-00041 TABLE 2396 DLBCL/BL FL FH MCL SLL Unclassified Total
% Correct % Unclassified % Error DLBCL/BL 249 6 0 0 0 7 262 95% 2%
3% FL 5 154 0 0 0 14 173 89% 8% 3% FH 0 0 17 0 0 0 17 100% 0% 0%
MCL 0 0 0 22 0 0 22 100% 0% 0% SLL 0 0 0 0 14 0 14 100% 0% 0%
TABLE-US-00042 TABLE 2397 DLBCL/BL FL FH MCL SLL Unclassified Total
% Correct % Unclassified % Error ABC 78 0 0 0 0 0 78 100% 0% 0% GCB
77 4 0 0 0 4 85 91% 5% 5% PMBL 33 0 0 0 0 0 33 100% 0% 0%
Unclassified 27 1 0 0 0 2 30 90% 7% 3% DLBCL DLBCL (not yet 14 0 0
0 0 1 15 93% 7% 0% subclassed) BL 20 1 0 0 0 0 21 95% 0% 5% FL
grade 1 1 78 0 0 0 3 82 95% 4% 1% FL grade 2 2 58 0 0 0 3 63 92% 5%
3% FL grade 3A 2 18 0 0 0 8 28 64% 29% 7% Combined FL 5 154 0 0 0
14 173 89% 8% 3% grades 1, 2, 3A FL grade 3B 2 1 0 0 0 4 7 14% 57%
29% FL unknown grade 3 11 0 0 0 0 14 79% 0% 21% FH 0 0 17 0 0 0 17
100% 0% 0% MCL 0 0 0 22 0 0 22 100% 0% 0% SLL 0 0 0 0 14 0 14 100%
0% 0%
[0287] As seen in Table 2396, perfect prediction of SLL, MCL, and
FH samples was obtained. The success rate for predicting FL and the
aggressive lymphomas (DL0CUBL) was also very good, with only 3% of
the samples being classified incorrectly. As seen in Table 2397,
perfect prediction was also obtained for ABC and PMBL samples
within the DLBCL samples.
Example 18
Classification of DLBCL/BL Samples Into Subtypes Based on Bayesian
Analysis of Gene Expression Data from the Lymph Dx Microarray
[0288] Samples identified as DLBCL/BL in Example 17 were subdivided
into four types: ABC, GCB, PMBL, and BL. These samples were then
used to generate six pair-wise models using the same procedure
described in Example 17. The results of the leave-one-out
predictions using these pair-wise models are set forth in Table
2398, below. Those results are also summarized in FIG. 28. The rows
in the table correspond to different sample groups, while the
columns indicate the prediction results. In this stage, the ability
of the prediction method to identify BL was again measured against
the diagnoses of hematopathologists. The ability of the prediction
method to identify the various DLBCL subtypes, on the other hand,
was measured against previous studies in which this distinction
belween subtypes was based on gene expression data from a
Lymphochip microarray (Alizadeh 2000, Rosenwald 2002, Rosenwald
2003a, Wright 2003).
TABLE-US-00043 TABLE 2398 ABC GCB PMBL BL Unclassified Total %
Correct % Unclassified % Error ABC 76 0 0 0 2 78 97% 3% 0% GCB 1 66
2 4 4 77 86% 9% 5% PMBL 0 2 27 0 4 33 82% 12% 6% Unclassified DLBCL
5 9 1 1 11 27 NA 41% 4% DLBCL (not yet 5 5 0 1 3 14 NA 21% 7%
subclassed) BL 0 1 0 18 1 20 90% 5% 5% FL grade 1 0 1 0 0 0 1 FL
grade 2 0 1 0 0 1 2 FL grade 3A 0 2 0 0 0 2 Combined FL grades 1,
2, 3A 0 4 0 0 1 5 FL grade 3B 0 1 0 0 1 2 FL unknown grade 0 1 0 1
1 3
[0289] As seen in Table 2398, only 1 of the 20 BL lymphoma samples
was classified incorrectly. The classification of DLBCL into
subtypes was also quite effective. All previously identified ABC
subtype samples were again assigned to the ABC subtype, while only
5% of the GCB samples and 6% of the PMBL samples were assigned to a
different subtype than they were assigned to previously.
[0290] The above classification was Implemented using S+ software
end the S+ subtype predictor script contained in the file entitled
"Subtype_Predictor.txt," located in the computer program
listing-appendix contained on CD number 22 of 22. This S+ script
implements the lymphoma prediction algorithm. When this script is
pasted into an S+ script window and run in a working directory
containing the data set files discussed below, it will produce a
text file entitled "PredictionResults.txt," which indicates the
results of the predictive algorithm. The other files in the
computer program listing appendix contain the required data sets.
In their required format, for carrying out the lymphoma type
Identification described above. The file entitled "GeneData.txt"
contains the gene expression values for each sample analyzed. This
file is included in the working directory when the S+ subtype
predictor script is run. The file entitled "GeneID.txt" contains
information about the genes in the GeneData.txt file, and is also
included in the working directory when the S+ subtype predictor
script is run. This file indicates the UNIQID for each gene, as
well as the extent to which the gene is associated with the lymph
node and proliferation signatures ("LN.cor" and "pro.cor,"
respectively). The file entitled "SampleID.txt" contains
information about the samples included in the "GeneData.txt" file,
specifically the original classification of all the samples. This
file is also included in the working directory when the S+ subtype
predictor script is run. The file entitled "PredictionResults.txt"
is an example of the productive output of the prediction
algorithm.
[0291] After the above model was validated using leave-one-out
cross-validation, the model was re-fit using all of the data to
generate a final predictor that could be applied to a new set of
data. Tables 2399-2414 indicate for each of the pair wise models
the list of genes used, the weight given to each of those genes,
the signature with which each gene was associated, the mean values
and covariance matrices associated with the subtypes being
compared, and the q-value cut-points of the pair-wise model.
TABLE-US-00044 TABLE 2399 ABC vs. BL Unigene ID Build 167 Signature
Scale UNIQID http://www.ncbi.nlm.nih.gov/UniGene Probe set Gene
symbol Standard -18.87 1101149 517226 229437_at BIC Standard -17.4
1121452 227817 205681_at BCL2A1 Standard -16.42 1123163 421342
208991_at STAT3 Standard -16.2 1121629 41691 205965_at BATF
Standard -15 1134095 89555 208018_s_at HCK Standard -14.75 1132636
306278 204490_s_at CD44 Standard -14.33 1119939 170087 202820_at
AHR Standard -14.25 1100138 278391 228234_at TIRP Standard -14.02
1128626 501452 219424_at EB13 Standard -13.89 1132883 432453
205027_s_at MAP3K8 Standard -13.88 1134991 444105 209474_s_at
ENTPD1 Standard -13.37 1109913 355724 239629_at CFLAR Standard
-13.25 1120389 75367 203761_at SLA Standard -12.99 1131497 114931
202295_s_at CTSH Standard -12.71 1115071 390476 223218_s_at MAIL
Standard -12.46 1136329 132739 211675_s_at HIC Standard -12.41
1128195 115325 218699_at RAB7L1 Standard -12.37 1124381 440808
212288_at FNBP1 Standard -12.30 1100562 26608 228737_at C20orf100
Standard -12.24 1101272 179089 229584_at DKFZp434 Standard -12.18
1128536 21126 219279_at DOCK10 Standard -11.64 1098271 300670
226056_at CDGAP Standard -11.41 1119566 433506 201954_at ARPC1B
Standard -11.11 1120651 80205 204269_at PIM2 Standard -10.89
1098952 62264 226841_at KIAA0937 Standard -10.80 1099939 488173
227983_at MGC7036 Standard -10.67 1134270 352119 208284_x_at GGT1
Standard -10.44 1134145 4750 208091_s_at DKFZP564 Standard -10.39
1123437 73090 209636_at NFKB2 Standard -10.17 1119884 418004
202716_at PTPM1 Standard -10.14 1129269 62919 220358_at SNFT
Standard -10.13 1126293 504816 215348_at TNFRSF5 Standard -10.12
1112344 163242 242408_at Standard -10.10 1135550 221811 210550_s_at
RASGRF1 Standard -10.08 1135165 170359 209827_s_at IL16 Standard
-10.05 1120808 127686 204562_at IRF4 Standard -10.01 1122067 72927
206693_at IL7 Standard -9.97 1132004 415117 203217_s_at SIAT9
Standard -9.86 1114824 193370 222762_x_at LIMD1 Standard -9.87
1132034 410455 203271_s_at UNC119 Standard -9.87 1099680 210387
227677_at JAK3 Standard -9.86 1132830 31210 204908_s_at BCL3
Standard -9.79 1099631 367639 227624_at FLJ20032 Standard -9.78
1120267 256278 203508_at TNFRSF1B Standard -9.77 1124167 378738
211986_at MGC5395 Standard -9.73 1108970 140489 238604_at Standard
-9.71 1136216 512152 211528_x_at HLA-G Standard -9.71 1120993 327
204912_at IL10RA Standard -9.68 1100847 97411 229070_at C6orf105
Standard -9.64 1123413 418291 209575_at IL10RB Standard -9.62
1115704 350268 224569_s_at IRF2BP2 Standard -9.58 1108237 126232
237753_at Standard -9.55 1121695 511759 206082_at HCP5 Standard
-9.48 1101905 170843 230345_at Standard -9.42 1119243 440165
201171_at ATP6V0E Standard -9.39 1140457 210546 221658_s_at IL21R
Standard -9.32 1098506 193400 226333_at IL6R Standard -9.31 1139805
414362 220230_s_at CYB5R2 Standard -9.30 1139037 173380 218223_s_at
CKIP-1 Standard -9.28 1130533 76507 200706_s_at LITAF Standard
-9.15 1098678 386140 226530_at BMF Standard -9.04 1133210 434374
205842_s_at JAK2 Standard 9.05 1116432 409362 229356_x_at KIAA1259
Standard 9.17 1097281 7037 224892_at PLDN Standard 9.17 1140018
438482 220917_s_at PWDMP Standard 9.30 1119997 367811 202951_at
STK38 Standard 9.41 1119817 409194 202561_at TNKS Standard 9.55
1139842 133523 220367_s_at SAP130 Standard 9.64 1132122 307734
203434_s_at MME Standard 9.77 1119258 88556 201209_at HDAC1
Standard 9.80 1128248 234149 218802_at FLJ20647 Standard 10.38
1101211 287659 229513_at STRBP Standard 10.52 1123419 170195
209590_at BMP7 Standard 10.71 1133755 404501 207318_s_at CDC2L5
Standard 10.80 1128192 102506 218696_at EIF2AK3 Standard 10.85
1124786 22370 212847_at NEXN Standard 10.92 1130114 445084
221965_at MPHOSPH9 Standard 11.00 1126081 309763 215030_at GRSF1
Standard 11.17 1118736 96731 38340_at HIP1R Standard 11.26 1124613
296720 212599_at AUTS2 Standard 11.43 1125456 300592 213906_at
MYBL1 Standard 11.60 1097177 9691 224761_at GNA13 Standard 12.11
1120400 152207 203787_at SSBP2 Standard 12.12 1139266 76640
218723_s_at RGC32 Standard 12.22 1100770 65578 228976_at Standard
12.73 1131246 153752 201853_s_at CDC25B Standard 13.48 1096503
21379 223522_at C9orf45 Standard 14.50 1124920 6150 213039_at
ARHGEF1 Standard 15.03 1128360 445043 218988_at SLC35E3 Standard
15.24 1099444 434489 227407_at FLJ90013 Standard 21.03 1134582
78202 208794_s_at SMARCA4 Standard Mean ABC -4179.76 Cut 1 0.20
Mean BL -1894.68 Cut 2 0.80 Covariance ABC 53707.58 Covariance BL
194887.5
TABLE-US-00045 TABLE 2400 ABC vs. GCB Unigene ID Build 167
Signature Scale UNIQID http://www.ncbi.nlm.nih.gov/UniGene Probe
set Gene symbol Standard -15.31 1122645 158341 207641_at TNFRSF13B
Standard -14.56 1120651 80205 204269_at PIM2 Standard -14.18
1120808 127686 204562_at IRF4 Standard -13.84 1114824 193370
222762_x_at LIMD1 Standard -13.44 1136687 59943 212345_s_at CREB3L2
Standard -13.12 1139805 414362 220230_s_at CYB5R2 Standard -12.23
1104552 193857 233483_at LOC96597 Standard -12.19 1097236 235860
224837_at FOXP1 Standard -12.06 1121629 41691 205965_at BATF
Standard -11.93 1128195 115325 218699_at RAB7L1 Standard -11.72
1111503 502910 241383_at KBRAS2 Standard -11.66 1134991 444105
209474_s_at ENTPD1 Standard -11.27 1098678 386140 226530_at BMF
Standard -10.9 1131074 76894 201572_x_at DCTD Standard -10.82
1135165 170359 209827_s_at IL16 Standard -10.7 1132396 118722
203988_s_at FUT8 Standard -10.54 1131541 310230 202369_s_at TRAM2
Standard -10.47 1105759 171262 235056_at ETV6 Standard -10.38
1121564 437783 205865_at ARID3A Standard -10.16 1130472 192374
200599_s_at TRA1 Standard -10.04 1132058 181999 203313_s_at TGIF
Standard -10.03 1105684 195155 234973_at SLC38A5 Standard -9.95
1097735 26765 225436_at LOC58489 Standard -9.94 1115071 390476
223218_s_at MAIL Standard -9.85 1101149 517226 229437_at BIC
Standard -9.83 1119884 418004 202716_at PTPN1 Standard -9.71
1134095 89555 208018_s_at HCK Standard -9.68 1135550 221811
210550_s_at RASGRF1 Standard -9.61 1098927 356216 226811_at
FLJ20202 Standard -9.6 1120389 75367 203761_at SLA Standard -9.58
1133910 167746 207655_s_at BLNK Standard 9.56 1118736 96731
38340_at HIP1R Standard 9.58 1128860 323634 219753_at STAG3
Standard 9.68 1134582 78202 208794_s_at SMARCA4 Standard 9.7
1121853 98243 206310_at SPINK2 Standard 10.14 1119256 88556
201209_at HDAC1 Standard 10.19 1132122 307734 203434_s_at MME
Standard 10.23 1120400 152207 203767_at SSBP2 Standard 10.48
1529344 317970 Lymph_Dx_065_at SERPINA11 Standard 10.64 1124613
296720 212599_at AUTS2 Standard 10.72 1132159 147868 203521_s_at
ZNF318 Standard 10.98 1097901 266175 225626_at PAG Standard 11.1
1128287 300063 218862_at ASB13 Standard 12.26 1099686 117721
227684_at Standard 12.45 1112674 310320 242794_at MAML3 Standard
13.15 1120370 78877 203723_at ITPKB Standard 14.23 1125456 300592
213906_at MYBL1 Lymph Node 6.8 1097202 386779 224796_at DDEF1 Lymph
Node 6.85 1131755 241257 202729_s_at LTBP1 Lymph Node 7.27 1136273
13775 211597_s_at HOP Lymph Node 7.35 1119424 75485 201599_at OAT
Lymph Node 7.86 1095985 83883 222450_at TMEPAI Lymph Node 8.02
1124875 18166 212975_at KIAA0870 Lymph Node 8.32 1124655 79299
212658_at LHFPL2 Lymph Node 8.62 1115034 387222 223158_s_at NEK6
Proliferation -9.11 1120583 153768 204133_at RNU3IP2 Proliferation
-7.87 1135492 408615 210448_s_at P2RX5 Proliferation -7.68 1127756
313544 217850_at NS Proliferation -7.57 1097195 149931 224785_at
MGC29814 Proliferation -7.31 1127813 14317 217962_at NOLA3
Proliferation -7.24 1138944 84753 218051_s_at FLJ12442
Proliferation -6.99 1139226 266514 218633_x_at FLJ11342
Proliferation -6.7 1137486 441069 214442_s_at MIZ1 Proliferation
-6.51 1133786 153591 207396_s_at ALG3 Proliferation -6.45 1131150
75514 201695_s_at NP Proliferation -6.45 1119076 268849 200681_at
GLO1 Proliferation -6.38 1115679 8345 224523_s_at MGC4308
Proliferation -6.34 1110223 212709 239973_at Proliferation -6.3
1529338 284275 Lymph_Dx_058_s_at PAK2 Proliferation -6.24 1135164
458360 209825_s_at UMPK Proliferation -6.24 1128738 335550
219581_at MGC2776 Proliferation -6.01 1099088 14355 226996_at
Proliferation -5.98 1123192 315177 209100_at IFRD2 Proliferation
-5.83 1116073 146161 227103_s_at MGC2408 Proliferation 5.79 1097388
278839 225024_at C20orf77 Proliferation 6.13 1124563 249441
212533_at WEE1 Standard Lymph Node Proliferation Mean ABC -2226.57
476.67 -1096.34 Cut 1 0.50 Mean GCB -1352.02 547.18 -1005.72 Cut 2
0.74 Covariance ABC 33472.10 3418.91 4347.99 3418.91 1296.05 846.32
4347.99 846.32 1609.13 Covariance GCB 53751.59 466.34 751.08 466.34
777.74 249.29 751.08 249.29 1708.67
TABLE-US-00046 TABLE 2401 ABC vs. PMBL Unigene ID Build 167
Signature Scale UNIQID http://www.ncbi.nlm.nih.gov/UniGene Probe
set Gene Symbol Standard -14.61 1097236 235860 224837_at FOXP1
Standard -14.47 1104552 193857 233483_at LOC96597 Standard -13.62
1122645 158341 207641_at TNFRSF13B Standard -12.05 1135102 349845
209685_s_at PRKCB1 Standard -11.65 1096499 293867 223514_at CARD11
Standard -11.26 1124770 153261 212827_at IGHM Standard -11.25
1125010 43728 213170_at GPX7 Standard -11.13 1109545 63187
239231_at Standard -10.99 1109220 445977 238880_at GTF3A Standard
-10.87 1131074 76894 201572_x_at DCTD Standard -10.68 1134517 75807
208690_s_at PDLIM1 Standard -10.63 1098604 32793 226444_at SLC39A10
Standard -10.56 1131219 109150 201810_s_at SH3BP5 Standard -10.52
1120651 80205 204269_at PIM2 Standard -10.39 1133910 167746
207655_s_at BLNK Standard -10.32 1099396 435949 227346_at ZNFN1A1
Standard -10.25 1529297 132335 Lymph_Dx_015_at Standard -10.17
1107575 424589 237033_at MGC52498 Standard -10.11 1117211 356509
233955_x_at HSPC195 Standard 10.06 1129517 -33 220712_at Standard
10.29 1139950 437385 220731_s_at FLJ10420 Standard 10.35 1097553
197071 225214_at PSMB7 Standard 10.41 1119516 6061 201834_at PRKAB1
Standard 10.47 1122772 66742 207900_at CCL17 Standard 10.55 1132762
80395 204777_s_at MAL Standard 10.77 1099265 375762 227193_at
Standard 10.81 1095996 288801 222482_at SSBP3 Standard 11.14
1100770 65578 228976_at Standard 11.19 1133801 181097 207426_s_at
TNFSF4 Standard 11.61 1099154 97927 227066_at MOBKL2C Standard
11.63 1120370 78877 203723_at ITPKB Standard 11.8 1112674 310320
242794_at MAML3 Standard 12.57 1105178 283961 234284_at GNG8
Standard 12.63 1124613 296720 212599_at AUTS2 Standard 13.28
1106415 169071 235774_at Standard 13.3 1121762 32970 206181_at
SLAMF1 Standard 13.6 1121853 98243 206310_at SPINK2 Lymph Node
10.91 1105838 129837 235142_at ZBTB8 Lymph Node 10.99 1136273 13775
211597_s_at HOP Lymph Node 11.02 1099418 172792 227370_at KIAA1946
Lymph Node 11.46 1124875 18166 212975_at KIAA0870 Lymph Node 11.99
1120299 79334 203574_at NFIL3 Lymph Node 12.49 1135871 104717
211031_s_at CYLN2 Lymph Node 13.33 1121767 458324 206187_at PTGIR
Proliferation -13.17 1138944 84753 218051_s_at FLJ12442
Proliferation -11.61 1116122 42768 227408_s_at DKFZp761O0113
Proliferation -11.16 1110223 212709 239973_at Proliferation -9.93
1120717 444159 204394_at SLC43A1 Proliferation -9.54 1110099 116665
239835_at TA-KRP Proliferation -9.49 1130942 445977 201338_x_at
GTF3A Proliferation -9.28 1123192 315177 209100_at IFRD2
Proliferation -9.14 1135492 408615 210448_s_at P2RX5 Proliferation
-9.03 1120011 3068 202983_at SMARCA3 Proliferation -9.01 1096738
87968 223903_at TLR9 Proliferation -8.91 1108961 292088 238593_at
FLJ22531 Standard Lymph Node Proliferation Mean ABC -849.47 531.79
-1027.48 Cut 1 0.20 Mean PMBL 27.99 750.84 -872.43 Cut 2 0.80
Covariance ABC 14028.46 3705.84 3118.60 3705.84 2326.91 1083.37
3118.60 1083.37 1589.42 Covariance PMBL 19425.29 5109.98 2199.28
5109.98 2084.28 620.86 2199.28 620.86 1028.44
TABLE-US-00047 TABLE 2402 BL vs. GCB Unigene ID Build 167 Signature
Scale UNIQID http://www.ncbi.nlm.nih.gov/UniGene Probe set Gene
Symbol Standard -12.78 1131246 153752 201853_s_at CDC25B Standard
-11.35 1099444 434489 227407_at FLJ90013 Standard -10.4 1116432
409362 229356_x_at KIAA1259 Standard -10.3 1134582 78202
208794_s_at SMARCA4 Standard -10.01 1133998 76884 207826_s_at ID3
Standard -9.3 1126081 309763 215030_at GRSF1 Standard -9.19 1096503
21379 223522_at C9orf45 Standard -8.95 1529340 -99 Lymph_Dx_061_at
Standard -8.88 1138128 390428 216199_s_at MAP3K4 Standard -8.8
1099152 351247 227064_at MGC15396 Standard -8.69 1133757 6113
207320_x_at STAU Standard -8.54 1116593 422889 230329_s_at NUDT6
Standard -8.4 1130926 508741 201310_s_at C5orf13 Standard -8.39
1135685 371282 210776_x_at TCF3 Standard -8.39 1140520 11747
221741_s_at C20orf21 Standard -8.34 1119802 7370 202522_at PITPNB
Standard -8.31 1096149 410205 222824_at NUDT5 Standard -8.23
1124786 22370 212847_at NEXN Standard -8.07 1098012 355669
225756_at CSNK1E Standard -7.89 1116317 526415 228661_s_at Standard
-7.86 1109195 416155 238853_at Standard -7.71 1134880 168799
209265_s_at METTL3 Standard -7.66 1529298 136707 Lymph_Dx_016_at
Standard -7.55 1128660 413071 219471_at C13orf18 Standard -7.55
1138973 11270 218097_s_at C10orf66 Standard -7.46 1127294 421986
217028_at CXCR4 Standard 7.47 1134270 352119 208284_x_at GGT1
Standard 7.48 1120743 79197 204440_at CD83 Standard 7.5 1098179
163725 225956_at LOC153222 Standard 7.55 1121400 223474 205599_at
TRAF1 Standard 7.59 1114967 7905 223028_s_at SNX9 Standard 7.6
1122087 72927 206693_at IL7 Standard 7.64 1101905 170843 230345_at
Standard 7.77 1120700 410745 204362_at SCAP2 Standard 7.8 1120572
84 204116_at IL2RG Standard 7.84 1098271 300670 226056_at CDGAP
Standard 7.9 1115073 131315 223220_s_at BAL Standard 7.9 1133210
434374 205842_s_at JAK2 Standard 8 1129289 62919 220358_at SNFT
Standard 8.01 1131940 1103 203085_s_at TGFB1 Standard 8.07 1098506
193400 226333_at IL6R Standard 8.13 1120601 441129 204166_at
KIAA0963 Standard 8.21 1102540 434881 231093_at FCRH3 Standard 8.24
1121695 611759 206082_at HCP5 Standard 8.33 1136877 409934
212998_x_at HLA-DQB1 Standard 8.37 1100138 278391 228234_at TIRP
Standard 8.46 1126293 504816 215346_at TNFRSF5 Standard 8.46
1127805 360627 217947_at CKLFSF6 Standard 8.59 1136573 914
211991_s_at HLA-DPA1 Standard 8.62 1119111 35052 200804_at TEGT
Standard 8.7 1136329 132739 211675_s_at HIC Standard 8.74 1123690
111805 210176_at TLR1 Standard 8.81 1138677 390440 217436_x_at
Standard 8.89 1113993 131811 244286_at Standard 8.89 1132651 439767
204529_s_at TOX Standard 8.91 1119566 433506 201954_at ARPC1B
Standard 9.01 1128626 501452 219424_at EBI3 Standard 9.17 1101272
179089 229584_at DKFZp434H2111 Standard 9.33 1136777 387679
212671_s_at HLA-DQA1 Standard 9.33 1109756 530304 239453_at
Standard 9.4 1136216 512152 211528_x at HLA-G Standard 9.4 1124381
440808 212288_at FNBP1 Standard 9.46 1099680 210387 227677_at JAK3
Standard 9.49 1109913 355724 239629_at CFLAR Standard 9.56 1132636
306278 204490_s_at CD44 Standard 9.59 1119243 440165 201171_at
ATP6V0E Standard 9.72 1101149 517226 229437_at BIC Standard 9.8
1130674 381008 200905_x_at HLA-E Standard 10.34 1119939 170087
202820_at AHR Standard 10.44 1132883 432453 205027_s_at MAP3K8
Standard 10.74 1121452 227817 205681_at BCL2A1 Standard 10.84
1137360 429658 214196_s_at CLN2 Standard 12.08 1132520 283063
204249_s_at LMO2 Standard 12.33 1131497 114931 202295_s_at CTSH
Standard 13.58 1123163 421342 208991_at STAT3 Lymph Node -9.1
1138136 433574 216215_s_at RBM9 Lymph Node 8.78 1130121 411958
221978_at HLA-F Lymph Node 9.22 1139830 221851 220330_s_at SAMSN1
Lymph Node 9.23 1131705 386467 202638_s_at ICAM1 Lymph Node 9.62
1130168 75626 222061_at CD58 Lymph Node 9.66 1121844 83077
206295_at IL18 Lymph Node 9.68 1121000 519033 204924_at TLR2 Lymph
Node 9.83 1102437 437023 230966_at IL4I1 Lymph Node 10.71 1119475
296323 201739_at SGK Lymph Node 11.09 1131786 375957 202803_s_at
ITGB2 Proliferation -11.07 1133141 344524 205677_s_at DLEU1
Proliferation -10.04 1138259 89525 216484_x_at HDGF Proliferation
-9.74 1131578 202453 202431_s_at MYC Proliferation -9.45 1137449
223745 214363_s_at MATR3 Proliferation -9.43 1130468 166463
200594_x_at HNRPU Proliferation -9.21 1138157 82563 216251_s_at
KIAA0153 Proliferation -9.15 1127756 313544 217850_at NS
Proliferation -9 1130433 246112 200058_s_at U5-200KD Proliferation
-8.76 1123108 108112 208828_at POLE3 Proliferation -8.75 1128738
335550 219581_at MGC2776 Proliferation -8.74 1122400 439911
207199_at TERT Proliferation -8.66 1097948 69476 225684_at
LOC348235 Proliferation -8.6 1119460 76122 201696_at SFRS4
Proliferation -8.6 1136401 27258 211761_s_at SIP Proliferation
-8.58 1099088 14355 226996_at Proliferation -8.51 1134653 253536
208901_s_at TOP1 Proliferation -8.49 1140584 294083 221932_s_at
C14orf87 Proliferation -8.43 1121309 23642 205449_at HSU79266
Proliferation -8.43 1120385 36708 203755_at BUB1B Proliferation
-8.38 1136710 75782 212429_s_at GTF3C2 Proliferation -8.36 1136605
448398 212064_x_at MAZ Proliferation -8.24 1120697 323462 204355_at
DHX30 Proliferation -8.19 1127833 382044 218001_at MRPS2
Proliferation -8.11 1096903 437460 224185_at FLJ10385 Proliferation
-8.1 1120596 4854 204159_at CDKN2C Proliferation -8.1 1120779 28853
204510_at CDC7 Standard Lymph Node Proliferation Mean BL 1098.69
576.05 -2392.12 Cut 1 0.09 Mean GCB 2187.37 768.53 -2129.35 Cut 2
0.53 Covariance BL 75263.67 12684.43 15734.77 12684.43 2650.81
2358.05 15734.77 2358.05 4653.00 Covariance GCB 50548.22 9301.12
14182.83 9301.12 2602.51 3028.21 14182.83 3028.21 5983.04
TABLE-US-00048 TABLE 2403 BL vs. PMBL Unigene ID Build 167
Signature Scale UNIQID http://www.ncbi.nlm.nih.gov/UniGene Probe
set Gene Symbol Standard -13.54 1099444 434489 227407_at FLJ90013
Standard -13.42 1096503 21379 223522_at C9orf45 Standard -13.36
1130114 445084 221965_at MPHOSPH9 Standard -13.27 1124786 22370
212847_at NEXN Standard -13.27 1134582 78202 208794_s_at SMARCA4
Standard -12.37 1096149 410205 222824_at NUDT5 Standard -11.95
1130855 77515 201189_s_at ITPR3 Standard -11.66 1529298 136707
Lymph_Dx_016_at Standard -11.35 1131246 153752 201853_s_at CDC25B
Standard -11.17 1136925 436939 213154_s_at BICD2 Standard -11.08
1124188 282346 211987_at TOP2B Standard -11.06 1133998 76884
207826_s_at ID3 Standard -10.76 1139266 76640 218723_s_at RGC32
Standard -10.74 1134880 168799 209265_s_at METTL3 Standard -10.69
1140520 11747 221741_s at C20orf21 Standard -10.6 1109545 63187
239231_at Standard -10.55 1106043 266331 235372_at FREB Standard
-10.52 1110214 144519 239964_at TCL6 Standard -10.49 1098592 283707
226431_at ALS2CR13 Standard -10.45 1109220 445977 238880_at GTF3A
Standard -10.41 1131263 249955 201877_s_at PPP2R5C Standard 10.54
1122772 66742 207900_at CCL17 Standard 10.59 1109913 355724
239629_at CFLAR Standard 10.82 1119884 418004 202716_at PTPN1
Standard 10.83 1135189 137569 209863_s_at TP73L Standard 10.89
1123437 73090 209636_at NFKB2 Standard 11.15 1124381 440806
212288_at FNBP1 Standard 11.26 1108237 126232 237753_at Standard
11.34 1101149 517226 229437_at BIC Standard 11.77 1139774 15827
220140_s_at SNX11 Standard 11.87 1123163 421342 208991_at STAT3
Standard 11.93 1129269 62919 220358_at SNFT Standard 12.03 1132636
306278 204490_s_at CD44 Standard 12.1 1138677 390440 217436_x_at
Standard 12.2 1139950 437385 220731_s_at FLJ10420 Standard 12.25
1134270 352119 208284_x_at GGT1 Standard 12.27 1136216 512152
211528_x_at HLA-G Standard 12.79 1121400 223474 205599_at TRAF1
Standard 12.82 1119939 170087 202820_at AHR Standard 13.12 1126293
504816 215346_at TNFRSF5 Standard 13.44 1100138 278391 228234_at
TIRP Standard 13.74 1132883 432453 205027_s_at MAP3K8 Standard
13.94 1131497 114931 202295_s_at CTSH Standard 14.15 1121762 32970
206181_at SLAMF1 Standard 14.51 1132520 283063 204249_s_at LMO2
Standard 14.68 1121452 227817 205681_at BCL2A1 Standard 15.24
1105178 283961 234284_at GNG8 Lymph Node 10.95 1121205 2488
205269_at LCP2 Lymph Node 11.22 1140845 21486 AFFX-HUMISGF3A/ STAT1
M97935_3_at Lymph Node 11.45 1131068 118400 201564_s_at FSCN1 Lymph
Node 11.92 1131705 386467 202638_s_at ICAM1 Lymph Node 12.06
1131038 81328 201502_s_at NFKBIA Lymph Node 12.49 1121444 153563
205668_at LY75 Lymph Node 13.01 1123457 446304 209684_at RIN2 Lymph
Node 13.19 1140404 354740 221584_s_at KCNMA1 Lymph Node 13.26
1124875 18166 212975_at KIAA0870 Lymph Node 14.06 1102437 437023
230966_at IL4I1 Lymph Node 14.11 1132766 82359 204781_s_at TNFRSF6
Lymph Node 15.31 1121767 458324 206187_at PTGIR Lymph Node 15.32
1135871 104717 211031_s_at CYLN2 Lymph Node 15.34 1138652 444471
217388_s_at KYNU Lymph Node 16.01 1139830 221851 220330_s_at SAMSN1
Standard Lymph Node Mean BL -66.97 1445.63 Cut 1 0.20 Mean PMBL
1205.38 2041.25 Cut 2 0.80 Covariance BL 35263.67 13424.88 13424.88
7458.56 Covariance PMBL 12064.38 5113.74 5113.74 3216.53
TABLE-US-00049 TABLE 2404 FH vs. DLBCL-BL Unigene ID Build 167
Signature Scale UNIQID http://www.ncbi.nlm.nih.gov/UniGene Probe
set Gene Symbol Standard -12.81 1104910 458262 233969_at IGL@
Standard -11.54 1102898 145519 231496_at FKSG87 Standard -11.46
1117298 449586 234366_x_at Standard -11.46 1132973 169294
205255_x_at TCF7 Standard -11.22 1133099 88646 205554_s_at DNASE1L3
Standard -10.76 1131531 153647 202350_s_at MATN2 Standard -10.59
1124283 406612 212144_at UNC84B Standard -10.35 1099847 36723
227867_at LOC129293 Standard -10.22 1136430 102950 211798_x_at
IGLJ3 Standard -10.05 1117394 -13 234792_x_at Standard -9.95
1133047 528338 205434_s_at AAK1 Standard -9.95 1098865 250905
226741_at LOC51234 Standard -9.82 1108515 98132 238071_at LCN6
Standard -9.8 1131407 154248 202125_s_at ALS2CR3 Standard -9.77
1128469 390817 219173_at FLJ22686 Standard -9.7 1123875 428
210607_at FLT3LG Standard -9.69 1131875 169172 202965_s_at CAPN6
Standard -9.69 1135173 3781 209841_s_at LRRN3 Standard -9.48
1099798 411081 227811_at FGD3 Standard -9.41 1119046 349499
200606_at DSP Standard -9.36 1122449 278694 207277_at CD209
Standard -9.34 1114017 133255 244313_at Standard -9.34 1122767 652
207892_at TNFSF5 Standard -9.24 1123369 79025 209481_at SNRK
Standard -9.16 1098954 128905 226844_at MOBKL2B Standard -9.14
1135513 421437 210481_s_at CD209L Standard -9.08 1100904 426296
229145_at LOC119504 Standard -8.99 1122738 81743 207840_at CD160
Standard -8.94 1120925 204891 204773_at IL11RA Standard 9.09
1123055 185726 208691_at TFRC Standard 9.62 1134858 405954
209226_s_at TNPO1 Standard 10.19 1123052 180909 208680_at PRDX1
Standard 10.81 1124178 446579 211969_at HSPCA Lymph Node -10.59
1137597 3903 214721_x_at CDC42EP4 Lymph Node -9.69 1119684 439586
202242_at TM4SF2 Lymph Node -9.25 1125593 8910 214180_at MAN1C1
Lymph Node -8.44 1124318 21858 212190_at SERPINE2 Lymph Node -8.09
1119448 212296 201656_at ITGA6 Lymph Node -8.07 1125546 125036
214081_at PLXDC1 Lymph Node -7.7 1097683 132569 225373_at PP2135
Lymph Node -7.56 1101305 112742 229623_at Lymph Node 7.45 1135240
436852 209955_s_at FAP Proliferation 6.97 1135101 20830 209680_s_at
KIFC1 Proliferation 7.03 1130426 432607 200039_s_at PSMB2
Proliferation 7.04 1130501 2795 200650_s_at LDHA Proliferation 7.08
1130744 158688 201027_s at EIF5B Proliferation 7.23 1137506 75258
214501_s_at H2AFY Proliferation 7.32 1131474 95577 202246_s_at CDK4
Proliferation 7.39 1130871 159087 201222_s_at RAD23B Proliferation
7.42 1119375 381072 201489_at PPIF Proliferation 7.47 1136595
404814 212038_s_at VDAC1 Proliferation 7.7 1135858 90093
211015_s_at HSPA4 Proliferation 7.78 1130527 184233 200692_s_at
HSPA9B Proliferation 7.78 1130820 151777 201144_s_at EIF2S1
Proliferation 7.83 1115829 433213 225253_s_at METTL2 Proliferation
7.84 1134699 439683 208974_x_at KPNB1 Proliferation 7.87 1120274
31584 203517_at MTX2 Proliferation 7.92 1136786 63788 212694_s_at
PCCB Proliferation 7.95 1097172 434886 224753_at CDCA5
Proliferation 8.4 1138537 -12 217140_s_at Proliferation 8.53
1119488 154672 201761_at MTHFD2 Proliferation 8.58 1130799 233952
201114_x_at PSMA7 Proliferation 8.72 1135673 82159 210759_s_at
PSMA1 Proliferation 9.4 1114679 16470 222503_s_at FLJ10904 Standard
Lymph Node Proliferation Mean FH -2193.59 -588.21 1571.78 Cut 1
0.50 Mean DLBCL-BL -1448.27 -441.91 1735.00 Cut 2 0.92 Covariance
FH 6729.73 1223.99 2541.22 1223.99 405.22 293.72 2541.22 293.72
1797.58 Covariance DLBCL-BL 17675.23 3642.41 4158.43 3642.41
1379.81 1066.48 4158.43 1066.48 2858.21
TABLE-US-00050 TABLE 2405 FH vs. FL Unigene ID Build 167 Signature
Scale UNIQID http://www.ncbi.nlm.nih.gov/UniGene Probe set Gene
Symbol Standard -11.23 1117298 449586 234366_x_at Standard -10.62
1121953 38365 206478_at KIAA0125 Standard -10.6 1104910 458262
233969_at IGL@ Standard -10.39 1136430 102950 211798_x_at IGLJ3
Standard -9.96 1129281 395486 220377_at C14orf110 Standard -9.73
1118835 102336 47069_at ARHGAP8 Standard -9.21 1127807 7236
217950_at NOSIP Standard -9.05 1128377 371003 219014_at PLAC8
Standard -8.85 1101004 2969 229265_at SKI Standard 9.06 1139411
368238 219073_s_at OSBPL10 Standard 9.07 1120789 154729 204524_at
PDPK1 Standard 9.21 1136464 159428 211833_s_at BAX Standard 9.29
1125279 445652 213575_at TRA2A Standard 9.45 1529390 79241
Lymph_Dx_120_at BCL2 Standard 9.52 1132022 173911 203247_s_at ZNF24
Standard 9.57 1139645 134051 219757_s_at C14orf101 Standard 9.64
1137561 67397 214639_s_at HOXA1 Standard 9.66 1114893 314623
222891_s_at BCL11A Standard 10.38 1098095 131059 225852_at ANKRD17
Standard 10.4 1134858 405954 209226_s_at TNPO1 Standard 12.65
1101054 173328 229322_at PPP2R5E Standard 12.79 1124178 446579
211969_at HSPCA Standard 13.34 1135489 288178 210438_x_at SSA2
Standard Mean FH 136.43 Cut 1 0.50 Mean FL 640.38 Cut 2 0.99
Covariance FH 10719.40 Covariance FL 9373.11
TABLE-US-00051 TABLE 2406 FH vs. MCL Unigene ID Build 167 Signature
Scale UNIQID http://www.ncbi.nlm.nih.gov/UniGene Probe set Gene
Symbol Standard 13.05 1100258 88442 228377_at KIAA1384 Standard
13.43 1529382 371468 Lymph_Dx_111_at CCND1 Standard 13.54 1106855
455101 236255_at KIAA1909 Standard 13.73 1529308 193014
Lymph_Dx_027_x_at Standard 14.56 1100873 445884 229103_at Standard
21.12 1132834 432638 204914_s_at SOX11 Lymph Node -8.44 1130378
234434 44783_s_at HEY1 Lymph Node -7.92 1123552 423077 209879_at
SELPLG Lymph Node -7.7 1131218 76753 201809_s_at ENG Lymph Node
-7.4 1097683 132569 225373_at PP2135 Lymph Node -7.15 1136273 13775
211597_s_at HOP Lymph Node 14.16 1134532 371468 208711_s_at CCND1
Standard Lymph Node Mean FH 451.68 -282.65 Cut 1 0.20 Mean MCFL
863.16 -156.82 Cut 2 0.80 Covariance FH 1617.92 222.89 222.89
271.65 Covariance MCL 3154.38 917.30 917.30 859.94
TABLE-US-00052 TABLE 2407 FH vs. SLL Unigene ID Build 167 Signature
Scale UNIQID http://www.ncbi.nlm.nih.gov/UniGene Probe set Gene
Symbol Standard -13.14 1120765 343329 204484_at PIK3C2B Standard
-12.9 1097897 266175 225622_at PAG Standard 12.72 1133195 274243
205805_s_at ROR1 Standard 12.74 1140416 58831 221601_s_at TOSO
Standard 13.53 1131687 359280 202606_s_at TLK1 Standard 13.57
1107044 163426 236458_at Standard 14.43 1529389 79241
Lymph_Dx_119_at BCL2 Standard 14.51 1129026 135146 220007_at
FLJ13984 Standard 14.77 1136987 21695 213370_s_at SFMBT1 Standard
14.79 1137109 469653 213689_x_at RPL5 Standard 15.37 1529308 193014
Lymph_Dx_027_x_at Standard 15.82 1120832 57856 204604_at PFTK1
Standard 17.37 1135550 221811 210550_s_at RASGRF1 Standard 18.98
1122864 434384 208195_at TTN Lymph Node -12.89 1123038 119000
208636_at ACTN1 Lymph Node -12.8 1130378 234434 44783_s_at HEY1
Lymph Node -11.59 1124875 18166 212975_at KIAA0870 Lymph Node
-11.47 1103497 50115 232231_at Lymph Node -10.31 1099358 93135
227300_at Lymph Node -10.27 1121129 285401 205159_at CSF2RB Lymph
Node -10.23 1100249 388674 228367_at HAK Lymph Node -10.05 1132345
109225 203868_s_at VCAM1 Lymph Node -9.93 1123401 50130 209550_at
NDN Lymph Node -9.75 1120500 82568 203979_at CYP27A1 Lymph Node
-9.57 1124318 21858 212190_at SERPINE2 Lymph Node -9.48 1120288
17483 203547_at CD4 Lymph Node -9.45 1123372 195825 209487_at RBPMS
Lymph Node -9.39 1123376 37682 209496_at RARRES2 Lymph Node -9.29
1123213 12956 209154_at TIP-1 Lymph Node -9.23 1098412 409515
226225_at MCC Lymph Node -9.23 1125593 8910 214180_at MAN1C1 Lymph
Node -9.17 1131786 375957 202803_s_at ITGB2 Lymph Node -9.04
1097683 132569 225373_at PP2135 Lymph Node -8.91 1097255 380144
224861_at Lymph Node -8.76 1131068 118400 201564_s_at FSCN1 Lymph
Node -8.7 1119074 54457 200675_at CD81 Lymph Node -8.68 1125130
35861 213338_at RIS1 Lymph Node -8.59 1139661 416456 219806_s_at
FN5 Standard Lymph Node Mean FH 1144.02 -2223.71 Cut 1 0.20 Mean
SLL 1592.27 -1798.11 Cut 2 0.80 Covariance FH 902.56 442.69 442.69
809.90 Covariance SLL 2426.26 2938.58 2938.58 9435.72
TABLE-US-00053 TABLE 2408 FL vs. DLBCL-BL Unigene ID Build 167
Signature Scale UNIQID http://www.ncbi.nlm.nih.gov/UniGene Probe
set Gene Symbol Standard -23.03 1124833 356416 212914_at CBX7
Standard -22.25 1099204 193784 227121_at Standard -22.2 1119766
93231 202423_at MYST3 Standard -22.04 1099798 411081 227811_at FGD3
Standard -22.01 1102898 145519 231496_at FKSG87 Standard -21.79
1131197 269902 201778_s_at KIAA0494 Standard -21.69 1098415 130900
226230_at KIAA1387 Standard -21.57 1120834 57907 204606_at CCL21
Standard -21.39 1130155 436657 222043_at CLU Standard -20.98
1100904 426296 229145_at LOC119504 Standard -20.8 1131531 153647
202350_s_at MATN2 Standard -20.72 1137582 433732 214683_s_at CLK1
Standard -20.66 1119782 155418 202478_at TRB2 Standard -20.59
1122767 652 207892_at TNFSF5 Standard -20.58 1125001 16193
213158_at Standard -20.56 1134921 413513 209341_s_at IKBKB Standard
-20.56 1132973 169294 205255_x_at TCF7 Standard -20.53 1136984
498154 213364_s_at SNX1 Standard -20.41 1115888 35096 225629_s_at
ZBTB4 Standard -20.37 1120160 436976 203288_at KIAA0355 Standard
-20.36 1139054 25726 218263_s_at LOC58486 Standard -20.31 1130030
301872 221834_at LONP Standard -20.08 1133024 436987 205383_s_at
ZNF288 Standard -20.05 1124666 526394 212672_at ATM Standard -19.3
1529397 406557 Lymph_Dx_127_s_at CLK4 Standard -19.16 1116056
243678 226913_s_at SOX8 Standard -19.14 1098433 202577 226250_at
Standard -19.1 1123635 408614 210073_at SIAT8A Standard -18.95
1138920 24395 218002_s_at CXCL14 Standard -18.84 1133099 88646
205554_s_at DNASE1L3 Standard -18.83 1098495 443668 226318_at TBRG1
Standard -18.64 1100879 119983 229111_at MASP2 Standard -18.59
1120695 385685 204352_at TRAF5 Standard -18.55 1119983 409783
202920_at ANK2 Standard -18.5 1101276 1098 229588_at ERdj5 Standard
-18.47 1099140 500350 227052_at Standard -18.46 1529331 374126
Lymph_Dx_051_s_at Standard -18.45 1131752 170133 202724_s_at FOXO1A
Standard -18.45 1099265 375762 227193_at Standard -18.32 1098179
163725 225956_at LOC153222 Standard -18.29 1119566 269777 201957_at
PPP1R12B Standard -18.19 1099900 444508 227934_at Standard -18.17
1119361 391858 201448_at TIA1 Standard -18.02 1121650 421137
206002_at GPR64 Standard -17.91 1100911 320147 229152_at C4orf7
Standard -17.86 1529285 348929 Lymph_Dx_002_at KIAA1219 Standard
-17.47 1529357 444651 Lymph_Dx_081_at Standard -17.42 1131883 2316
202936_s_at SOX9 Standard -17.16 1129943 512828 221626_at ZNF506
Standard -17.12 1121301 449971 205437_at ZNF134 Standard -17.11
1131340 437457 202018_s_at LTF Standard -17.1 1124606 444324
212588_at PTPRC Standard -17.08 1131407 154248 202125_s_at ALS2CR3
Standard -16.97 1118939 198161 60528_at PLA2G4B Standard -16.91
1134738 75842 209033_s_at DYRK1A Standard -16.9 1134083 285091
207996_s_at C18orf1 Standard -16.89 1120925 204891 204773_at IL11RA
Standard -16.86 1110070 -101 239803_at Standard -16.83 1100042
351413 228113_at RAB37 Standard -16.82 1120134 75545 203233_at IL4R
Standard -16.75 1124283 406612 212144_at UNC84B Standard -16.72
1109603 -100 239292_at Standard -16.71 1120509 155090 204000_at
GNB5 Standard -16.65 1133538 1416 206780_s_at FCER2 Standard -16.64
1130735 179526 201009_s_at TXNIP Standard -16.59 1100150 9343
228248_at MGC39830 Standard -16.54 1124237 258855 212080_at MLL
Standard -16.51 1124416 283604 212331_at RBL2 Standard -16.48
1133091 73792 205544_s_at CR2 Standard -16.46 1131263 249955
201877_s_at PPP2R5C Standard -16.44 1118347 528404 243366_s_at
ITGA4 Standard -16.43 1529343 521948 Lymph_Dx_064_at Standard
-16.43 1099549 446665 227533_at Standard 17.05 1529453 372679
Lymph_Dx_085_at FCGR3A Standard 17.41 1097540 388087 225195_at
Standard 18.47 1140473 17377 221676_s_at CORO1C Standard 18.55
1121100 301921 205098_at CCR1 Standard 20.07 1124254 301743
212110_at SLC39A14 Standard 20.2 1130771 61153 201068_s_at PSMC2
Standard 21.46 1137583 273415 214687_x_at ALDOA Standard 21.55
1098168 22151 225943_at NLN Standard 24.07 1123055 185726 208691_at
TFRC Standard 24.09 1123052 180909 208680_at PRDX1 Lymph Node -20.5
1137597 3903 214721_x_at CDC42EP4 Lymph Node -18.52 1124318 21858
212190_at SERPINE2 Lymph Node -18.5 1136762 380138 212624_s_at CHN1
Lymph Node -18.07 1101305 112742 229623_at Lymph Node -17.75
1100249 388674 228367_at HAK Lymph Node -16.1 1098412 409515
226225_at MCC Lymph Node -15.61 1140464 111676 221667_s_at HSPB8
Lymph Node -15.43 1136832 434959 212842_x_at RANBP2L1 Lymph Node
-15.37 1119684 439586 202242_at TM4SF2 Lymph Node -15.02 1097448
250607 225093_at UTRN Lymph Node -14.83 1136844 16007 212875_s_at
C21orf25 Lymph Node -14.73 1135056 169946 209604_s_at GATA3 Lymph
Node -14.48 1097202 386779 224796_at DDEF1 Lymph Node -14.44
1121278 21355 205399_at DCAMKL1 Lymph Node -14.22 1125009 27621
213169_at Lymph Node -13.97 1100288 26981 228411_at ALS2CR19 Lymph
Node -13.51 1132462 14845 204131_s_at FOXO3A Lymph Node -13.37
1135322 450230 210095_s_at IGFBP3 Lymph Node -13.35 1097280 423523
224891_at Lymph Node -12.86 1137097 20107 213658_s_at KNS2 Lymph
Node -12.85 1098809 359394 226682_at Lymph Node -12.28 1124875
18166 212975_at KIAA0870 Lymph Node -12.18 1132345 109225
203868_s_at VCAM1 Lymph Node -12 1097561 19221 225224_at
DKFZP566G1424 Lymph Node -11.71 1123401 50130 209550_at NDN Lymph
Node -11.04 1136996 283749 213397_x_at RNASE4 Lymph Node -10.77
1136788 355455 212698_s_at 36778 Lymph Node -10.71 1098822 443452
226695_at PRRX1 Lymph Node -10.63 1134200 90786 208161_s_at ABCC3
Lymph Node -10.47 1136427 276506 211795_s_at FYB Lymph Node -10.46
1121186 100431 205242_at CXCL13 Lymph Node -10.39 1099332 32433
227272_at Lymph Node -10.39 1098978 124863 226869_at Lymph Node
-10.22 1103303 49605 232000_at C9orf52 Lymph Node -10.16 1131325
13313 201990_s_at CREBL2 Lymph Node -10.16 1098174 274401 225949_at
LOC340371 Lymph Node -9.93 1124733 66762 212771_at LOC221061 Lymph
Node -9.42 1123372 195825 209487_at RBPMS Lymph Node -9.36 1132220
448805 203632_s_at GPRC5B Lymph Node -9.29 1120703 83974 204368_at
SLCO2A1 Lymph Node -9.26 1132013 434961 203232_s_at SCA1 Lymph Node
-9.25 1097307 379754 224929_at LOC340061 Lymph Node -9.18 1119251
433941 201194_at SEPW1 Lymph Node -9.08 1097609 6093 225283_at
ARRDC4 Lymph Node -9.07 1136459 252550 211828_s_at KIAA0551 Lymph
Node -8.86 1132775 1027 204803_s_at RRAD Lymph Node -8.78 1098946
135121 226834_at ASAM Lymph Node -8.68 1140589 433488 221942_s_at
GUCY1A3 Lymph Node -8.44 1116966 301124 232744_x_at Lymph Node
-8.39 1100130 76494 228224_at PRELP Lymph Node -8.36 1110019 -94
239744_at Lymph Node -8.3 1134647 298654 208892_s_at DUSP6 Lymph
Node -8.28 1125593 8910 214180_at MAN1C1 Lymph Node 7.97 1134370
1422 208438_s_at FGR Lymph Node 8.05 1123566 155935 209906_at C3AR1
Lymph Node 8.09 1131119 349656 201647_s_at SCARB2 Lymph Node 8.11
1123586 93841 209948_at KCNMB1 Lymph Node 8.13 1128615 104800
219410_at FLJ10134 Lymph Node 8.21 1097297 166254 224917_at VMP1
Lymph Node 8.23 1120299 79334 203574_at NFIL3 Lymph Node 8.37
1128157 23918 218631_at VIP32 Lymph Node 8.4 1130054 82547
221872_at RARRES1 Lymph Node 8.41 1098152 377588 225922_at KIAA1450
Lymph Node 8.53 1101566 98558 229947_at Lymph Node 8.59 1135251
21486 209969_s_at STAT1 Lymph Node 8.84 1099167 381105 227080_at
MGC45731 Lymph Node 9.01 1132920 753 205119_s_at FPR1 Lymph Node
9.26 1097253 77873 224859_at B7H3 Lymph Node 9.29 1120500 82568
203979_at CYP27A1 Lymph Node 9.36 1131507 172928 202311_s_at COL1A1
Lymph Node 9.38 1096456 82407 223454_at CXCL16 Lymph Node 9.49
1136172 38084 211470_s_at SULT1C1 Lymph Node 10.03 1138244 418138
216442_x_at FN1 Lymph Node 10.34 1134424 -17 208540_x_at S100A14
Lymph Node 10.48 1136152 458436 211434_s_at CCRL2 Lymph Node 10.51
1118708 7835 37408_at MRC2 Lymph Node 10.6 1136540 179657
211924_s_at PLAUR Lymph Node 10.63 1098278 166017 226066_at MITF
Lymph Node 10.76 1119477 163867 201743_at CD14 Lymph Node 10.81
1096429 64896 223405_at NPL Lymph Node 11.58 1123672 67846
210152_at LILRB4 Lymph Node 12 1096364 29444 223276_at NID67 Lymph
Node 12.16 1119070 446570 200663_at CD63 Lymph Node 12.3 1133065
77274 205479_s_at PLAU Lymph Node 12.5 1135240 436852 209955_s_at
FAP Lymph Node 13.09 1116826 26204 231823_s_at KIAA1295 Lymph Node
13.32 1119068 417004 200660_at S100A11 Lymph Node 13.45 1120266
246381 203507_at CD68 Lymph Node 13.63 1133216 502577 205872_x_at
PDE4DIP Lymph Node 13.67 1131815 386678 202856_s_at SLC16A3 Lymph
Node 14.38 1132132 279910 203454_s_at ATOX1 Lymph Node 15.25
1134682 411701 208949_s_at LGALS3 Lymph Node 15.46 1119237 389964
201141_at GPNMB Lymph Node 15.89 1137698 442669 215001_s_at GLUL
Lymph Node 17.8 1137782 384944 215223_s_at SOD2 Lymph Node 20.11
1130629 135226 200839_s_at CTSB Proliferation 21.02 1119375 381072
201489_at PPIF Proliferation 21.24 1119488 154872 201761_at MTHFD2
Proliferation 21.31 1119467 21635 201714_at TUBG1 Proliferation
21.68 1130820 151777 201144_s_at EIF2S1 Proliferation 21.69 1131474
95577 202246_s_at CDK4 Proliferation 22.2 1125249 244723 213523_at
CCNE1 Proliferation 22.97 1130501 2795 200650_s_at LDHA
Proliferation 23.12 1136913 99962 213113_s_at SLC43A3 Proliferation
24.05 1130426 432607 200039_s_at PSMB2 Standard Lymph Node
Proliferation Mean FL -11121.51 -1603.39 1890.60 Cut 1 0.34 Mean
DLBCL-BL -8760.65 -460.71 2101.10 Cut 2 0.94 Covariance FL
246359.77 111505.42 28908.20 111505.42 67036.17 13130.59 28908.20
13130.59 4617.24 Covariance DLBCL-BL 413069.12 178811.32 30151.89
178811.32 106324.53 10877.26 30151.89 10877.26 5180.68
TABLE-US-00054 TABLE 2409 FL vs. MCL Unigene ID Build 167 Signature
Scale UNIQID http://www.ncbi.nlm.nih.gov/UniGene Probe set Gene
Symbol Standard -24.56 1123731 17165 210258_at RGS13 Standard
-22.56 1133192 24024 205801_s_at RASGRP3 Standard -21.12 1114543
156189 244887_at Standard -18.49 1120090 155024 203140_at BCL6
Standard -18.07 1124646 436432 212646_at RAFTLIN Standard -17.24
1132122 307734 203434_s_at MME Standard -16.63 1105986 49614
235310_at GCET2 Standard -15.09 1120134 75545 203233_at IL4R
Standard -14.05 1132651 439767 204529_s_at TOX Standard 13.8
1098277 6786 226065_at PRICKLE1 Standard 13.85 1109560 207428
239246_at FARP1 Standard 13.86 1103504 142517 232239_at Standard
13.88 1132734 126248 204724_s_at COL9A3 Standard 13.91 1115905
301478 226757_s_at CLMN Standard 14.89 1098840 55098 226713_at
C3orf6 Standard 14.97 1100873 445884 229103_at Standard 14.99
1139393 170129 219032_x_at OPN3 Standard 16.13 1124864 411317
212960_at KIAA0882 Standard 16.36 1106855 455101 236255_at KIAA1909
Standard 16.43 1120858 410683 204647_at HOMER3 Standard 17.38
1130926 508741 201310_s_at C5orf13 Standard 18.3 1103711 288718
232478_at Standard 18.62 1109505 8162 239186_at MGC39372 Standard
20.31 1132834 432638 204914_s_at SOX11 Standard 22.61 1096070
241565 222640_at DNMT3A Standard 28.66 1529382 371468
Lymph_Dx_111_at CCND1 Lymph Node -10.77 1097202 386779 224796_at
DDEF1 Lymph Node -10.22 1119546 433898 201921_at GNG10 Lymph Node
-9.89 1132766 82359 204781_s_at TNFRSF6 Lymph Node -9.4 1138867
10706 217892_s_at EPLIN Lymph Node 9.65 1125025 301094 213196_at
Lymph Node 10.44 1134797 433394 209118_s_at TUBA3 Lymph Node 22.6
1529456 371468 Lymph_Dx_113_at CCND1 Proliferation -7.36 1097948
69476 225684_at LOC348235 Proliferation -7.31 1130747 234489
201030_x_at LDHB Proliferation -6.95 1130923 459987 201306_s_at
ANP32B Proliferation -6.87 1120205 5198 203405_at DSCR2
Proliferation -6.64 1132468 79353 204147_s_at TFDP1 Proliferation
-6.1 1119916 177584 202780_at OXCT Proliferation -6.08 1119873
446393 202697_at CPSF5 Proliferation -6.08 1119488 154672 201761_at
MTHFD2 Proliferation -6.04 1130658 447492 200886_s_at PGAM1
Proliferation -5.82 1132825 512813 204900_x_at SAP30 Proliferation
-5.53 1115607 435733 224428_s_at CDCA7 Proliferation -5.44 1120316
63335 203611_at TERF2 Proliferation -5.34 1114970 279529
223032_x_at PX19 Proliferation -5.32 1140843 169476
AFFX-HUMGAPDH/M33197_5_at GAPD Proliferation -5.28 1131081 180610
201586_s_at SFPQ Proliferation -5.15 1121062 408658 205034_at CCNE2
Proliferation 5.15 1120986 172052 204886_at PLK4 Proliferation 5.16
1097195 149931 224785_at MGC29814 Proliferation 5.2 1120011 3068
202983_at SMARCA3 Proliferation 5.47 1100183 180582 228286_at
FLJ40869 Proliferation 5.67 1121012 96055 204947_at E2F1
Proliferation 5.84 1115679 8345 224523_s_at MGC4308 Proliferation
5.88 1135285 449501 210024_s_at UBE2E3 Proliferation 5.92 1120520
35120 204023_at RFC4 Proliferation 6.16 1529361 388681
Lymph_Dx_086_s_at HDAC3 Proliferation 6.45 1096054 21331 222606_at
FLJ10036 Proliferation 6.45 1096738 87968 223903_at TLR9
Proliferation 6.51 1136781 120197 212680_x_at PPP1R14B
Proliferation 6.63 1119466 179718 201710_at MYBL2 Proliferation
6.65 1136285 182490 211615_s_at LRPPRC Proliferation 6.67 1136853
66170 212922_s_at SMYD2 Proliferation 7.45 1119390 77254 201518_at
CBX1 Proliferation 8.87 1116122 42768 227408_s_at DKFZp761O0113
Proliferation 10.12 1119515 3352 201833_at HDAC2 Standard Lymph
Node Proliferation Mean FL -18.82 -33.90 23.53 Cut 1 0.14 Mean MCL
1558.10 113.95 165.48 Cut 2 0.56 Covariance FL 21302.14 1098.24
678.04 1098.24 226.29 75.99 678.04 75.99 315.67 Covariance MCL
81008.29 5261.37 9185.20 5261.37 2047.34 875.56 9185.20 875.56
1447.43
TABLE-US-00055 TABLE 2410 FL vs. SLL Unigene ID Build 167 Signature
Scale UNIQID http://www.ncbi.nlm.nih.gov/UniGene Probe set Gene
Symbol Standard -21.04 1123731 17165 210258_at RGS13 Standard
-20.91 1124646 436432 212646_at RAFTLIN Standard -18.82 1099651
120785 227646_at EBF Standard -18.12 1114543 156189 244887_at
Standard -17.85 1105986 49614 235310_at GCET2 Standard -16.73
1100911 320147 229152_at C4orf7 Standard -15.77 1132122 307734
203434_s_at MME Standard -15.12 1120090 155024 203140_at BCL6
Standard -14.89 1097897 266175 225622_at PAG Standard -14.36
1529343 521948 Lymph_Dx_064_at Standard -14.32 1529318 291954
Lymph_Dx_038_at Standard -14.06 1128694 171466 219517_at ELL3
Standard -13.61 1101586 187884 229971_at GPR114 Standard -13.57
1119752 511745 202391_at BASP1 Standard -13.13 1137561 67397
214639_s_at HOXA1 Standard -12.85 1097247 388761 224851_at CDK6
Standard -12.43 1529344 317970 Lymph_Dx_065_at SERPINA11 Standard
-12.4 1120765 343329 204484_at PIK3C2B Standard -12.33 1130155
436657 222043_at CLU Standard -12.07 1529292 -92 Lymph_Dx_010_at
Standard -12.01 1119939 170087 202820_at AHR Standard -11.82
1119919 199263 202786_at STK39 Standard -11.77 1099686 117721
227684_at Standard -11.63 1119782 155418 202478_at TRB2 Standard
10.97 1529309 512797 Lymph_Dx_028_at HSH2 Standard 10.97 1139393
170129 219032_x_at OPN3 Standard 11.04 1131246 153752 201853_s_at
CDC25B Standard 11.07 1140391 44865 221558_s_at LEF1 Standard 11.16
1140418 58831 221601_s_at TOSO Standard 11.35 1127807 7236
217950_at NOSIP Standard 11.67 1529317 -98 Lymph_Dx_037_at Standard
11.81 1117343 306812 234643_x_at BUCS1 Standard 11.82 1102081
506977 230551_at Standard 11.82 1135042 79015 209582_s_at MOX2
Standard 11.96 1132734 126248 204724_s_at COL9A3 Standard 12.09
1137109 469653 213689_x_at RPL5 Standard 12.14 1099939 488173
227983_at MGC7036 Standard 12.19 1129103 99430 220118_at TZFP
Standard 12.47 1135592 758 210621_s_at RASA1 Standard 12.78 1108970
140489 238604_at Standard 12.92 1097143 74335 224716_at HSPCB
Standard 13.18 1136865 412128 212959_s_at MGC4170 Standard 13.96
1098220 80720 226002_at GAB1 Standard 14.06 1100847 97411 229070_at
C6orf105 Standard 14.39 1098865 250905 226741_at LOC51234 Standard
15.57 1136687 59943 212345_s_at CREB3L2 Standard 15.75 1107044
163426 236458_at Standard 16.52 1123622 8578 210051_at EPAC
Standard 17.74 1136987 21695 213370_s_at SFMBT1 Standard 19.15
1129026 135146 220007_at FLJ13984 Standard 19.65 1131854 414985
202923_s_at GCLC Lymph Node -14.99 1124875 18166 212975_at KIAA0870
Lymph Node -14.33 1099358 93135 227300_at Lymph Node -13.26 1121129
285401 205159_at CSF2RB Lymph Node -12.61 1119074 54457 200675_at
CD81 Lymph Node -12.52 1121029 412999 204971_at CSTA Lymph Node
-11.48 1137247 234734 213975_s_at LYZ Lymph Node -10.97 1128781
79741 219648_at FLJ10116 Lymph Node 11.79 1119880 442844 202709_at
FMOD Lymph Node 14.4 1134370 1422 208438_s_at FGR Standard Lymph
Node Mean FL -663.95 -730.08 Cut 1 0.20 Mean SLL 1332.84 -484.93
Cut 2 0.80 Covariance FL 37097.15 1710.73 1710.73 663.78 Covariance
SLL 85989.25 17661.52 17661.52 4555.06
TABLE-US-00056 TABLE 2411 GCB vs. PMBL Unigene ID Build 167
Signature Scale UNIQID http://www.ncbi.nlm.nih.gov/UniGene Probe
set Gene Symbol Standard -8.39 1096440 231320 223423_at GPR160
Standard -8.13 1096108 292871 222731_at ZDHHC2 Standard -8.12
1125231 446375 213489_at MAPRE2 Standard -8.02 1136759 188882
212605_s_at Standard -7.91 1096499 293867 223514_at CARD11 Standard
-7.8 1099388 124024 227336_at DTX1 Standard -7.71 1139623 193736
219687_s_at BANK1 Standard -7.68 1098592 283707 226431_at ALS2CR13
Standard -7.67 1107575 424589 237033_at MGC52498 Standard -7.63
1116829 115467 231840_x_at LOC90624 Standard -7.42 1130114 445084
221965_at MPHOSPH9 Standard -7.27 1098909 446408 226789_at Standard
7.34 1138759 396404 217707_x_at SMARCA2 Standard 7.37 1120355 80420
203687_at CX3CL1 Standard 7.4 1134270 352119 208284_x_at GGT1
Standard 7.44 1115441 5470 224156_x_at IL17RB Standard 7.78 1103054
341531 231690_at Standard 7.91 1119765 81234 202421_at IGSF3
Standard 7.92 1119438 118110 201641_at BST2 Standard 8.09 1135645
31439 210715_s_at SPINT2 Standard 8.15 1106015 96885 235343_at
FLJ12505 Standard 8.18 1121400 223474 205599_at TRAF1 Standard 8.38
1139950 437385 220731_s_at FLJ10420 Standard 8.73 1122112 1314
206729_at TNFRSF8 Standard 8.77 1122772 66742 207900_at CCL17
Standard 8.84 1132762 80395 204777_s_at MAL Standard 9.64 1139774
15827 220140_s_at SNX11 Standard 10.53 1133801 181097 207426_s_at
TNFSF4 Standard 11.52 1106415 169071 235774_at Standard 12.09
1129269 62919 220358_at SNFT Standard Mean GCB 292.76 Cut 1 0.16
Mean PMBL 725.28 Cut 2 0.50 Covariance GCB 8538.86 Covariance PMBL
11405.23
TABLE-US-00057 TABLE 2412 MCL vs. DLBCL-BL Unigene ID Build 167
Signature Scale UNIQID http://www.ncbi.nlm.nih.gov/UniGene Probe
set Gene Symbol Standard -26.11 1529382 371468 Lymph_Dx_111_at
CCND1 Standard -18.35 1103711 288718 232478_at Standard -17.03
1106855 455101 236255_at KIAA1909 Standard -16.49 1098840 55098
226713_at C3orf6 Standard -15.41 1109505 8162 239186_at MGC39372
Standard -15.11 1098954 128905 226844_at MOBKL2B Standard -14.96
1103504 142517 232239_at Standard -14.74 1096070 241565 222640_at
DNMT3A Standard -13.81 1137663 247362 214909_s_at DDAH2 Standard
-13.8 1124864 411317 212960_at KIAA0882 Standard -13.62 1140127
125300 221044_s_at TRIM34 Standard -13.62 1119361 391858 201448_at
TIA1 Standard -13.37 1127849 76691 218032_at SNN Standard 13.72
1133192 24024 205801_s_at RASGRP3 Standard 13.85 1137583 273415
214687_x_at ALDOA Standard 15.02 1123052 180909 208680_at PRDX1
Standard 16.21 1097611 438993 225285_at BCAT1 Lymph Node -19.18
1529456 371468 Lymph_Dx_113_at CCND1 Lymph Node -10.71 1098978
124863 226869_at Lymph Node -9.17 1097448 250607 225093_at UTRN
Lymph Node 8.84 1135240 436852 209955_s_at FAP Lymph Node 9.11
1119475 296323 201739_at SGK Lymph Node 9.22 1119237 389964
201141-art GPNMB Lymph Node 9.46 1130629 135226 200839_s_at CTSB
Lymph Node 10.1 1130054 82547 221872_at RARRES1 Standard Lymph Node
Mean MCL -1417.55 -25.58 Cut 1 0.50 Mean DLBCL-BL -756.07 202.29
Cut 2 0.88 Covariance MCL 15347.98 3525.48 3525.48 5420.31
Covariance DLBCL-BL 5132.06 1007.64 1007.64 991.38
TABLE-US-00058 TABLE 2413 MCL vs. SLL Unigene ID Build 167
Signature Scale UNIQID http://www.ncbi.nlm.nih.gov/UniGene Probe
set Gene Symbol Standard -20.18 1132834 432638 204914_s_at SOX11
Standard -15.17 1130926 508741 201310_s_at C5orf13 Standard 13.44
1116150 16229 227606_s_at AMSH-LP Standard 14.44 1120134 75545
203233_at IL4R Standard 15.18 1529437 445162 Lymph_Dx_175_at BTLA
Standard 15.19 1529317 -98 Lymph_Dx_037_at Standard 16.2 1135042
79015 209582_s_at MOX2 Standard Mean MCL 181.38 Cut 1 0.20 Mean SLL
564.92 Cut 2 0.80 Covariance MCL 1734.42 Covariance SLL 910.75
TABLE-US-00059 TABLE 2414 SLL vs. DLBCL-BL Unigene ID Build 167
Signature Scale UNIQID http://www.ncbi.nlm.nih.gov/UniGene Probe
set Gene Symbol Standard -16.014498 1123622 8578 210051_at EPAC
Standard -15.26356533 1102081 506977 230551_at Standard
-14.82150028 1107044 163426 236458_at Standard -14.17813266 1098865
260905 226741_at LOC51234 Standard -12.92844719 1110740 416810
240538_at Standard -12.86520757 1129026 135146 220007_at FLJ13984
Standard -12.2702748 1135592 758 210621_s_at RASA1 Standard
-11.87309449 1117343 306812 234643_x_at BUCS1 Standard -11.81789137
1136987 21695 213370_s_at SFMBT1 Standard -11.78631706 1124830 9059
212911_at KIAA0962 Standard -11.39454435 1133538 1416 206760_s_at
FCER2 Standard -11.39050362 1135802 439343 210944_s_at CAPN3
Standard 11.72928644 1120770 300825 204493_at BID Lymph Node
-12.21593247 1119880 442844 202709_at FMOD Lymph Node 9.514704847
1135240 436852 209955_s_at FAP Lymph Node 9.739298877 1096429 64896
223405_at NPL Lymph Node 10.05087645 1119475 296323 201739_at SGK
Lymph Node 13.11985922 1119237 389964 201141_at GPNMB Proliferation
10.47525875 1128106 14559 218542_at C10orf3 Proliferation
10.53295782 1132825 512813 204900_x_at SAP30 Proliferation
11.93918891 1130501 2795 200650_s_at LDHA Proliferation 11.98738778
1123439 287472 209642_at BUB1 Proliferation 11.99741644 1115607
435733 224428_s_at CDCA7 Standard Lymph Node Proliferation Mean SLL
-1383.640809 177.4452398 467.2463569 Cut 1 0.201266305 Mean
DLBCL-BL -926.7275468 329.6795845 582.9070266 Cut 2 0.799816116
Covariance SLL 3591.384775 1789.7516 856.0703202 1789.7516
1421.869535 663.4782048 856.0703202 663.4782048 965.6470151
Covariance DLBCL-BL 2922.643347 473.543487 634.3258773 473.543487
931.9845277 -53.85584619 634.3258773 -53.85584619 767.3545404
Example 19
Classification of Lymphoma Samples as BL or DLBCL Based on Bayesian
Analysis of Gene Expression Data from the Affymetrix U133 Plus 2.0
Microarray and the Lymphoma Microarray
[0292] Tumor biopsies were obtained from 71 previously untreated,
HIV-negative patients diagnosed with sporadic BL (54 cases) or
Burkitt-like lymphoma (17 cases) between 1986 and 2004 at seven
institutions belonging to the Leukemia Lymphoma Molecular Profiling
Project (LLMPP). In addition, 232 samples were obtained from
patients diagnosed with DLBCL, 223 of these were part of previously
published studies (Rosenwald 2002; Rosenwald 2003b) using the
Lymphochip microarray (Alizadeh 1999), while the other nine were
"high-grade" DLBCL samples with K167 scores (a measure of lymphoma
cell proliferation) of nearly 100%. All 303 cases were reviewed by
a panel of eight hematopathologists using current WHO criteria for
morphology, immunophenotype, and cytogenetics. Specifically,
specimens-classified as BL were required to have a c-myc
translocation, morphology consistent with BL, a K167+ proliferative
fraction of greater than 90%, and immunohistochemical evidence of
CD10 and/or BCL6 expression. Specimens were classified as DLBCL
based on morphological criteria and a B cell immunophenotype.
[0293] Among the 232 DLBCL cases, the median age at diagnosis was
61.5 years (range, 8.9 to 92 years). Median follow up was 2.5 years
(6.8 years for survivors). FISH for c-myc translocation was
performed in 87 cases, with six cases testing positive.
[0294] Among the 71 BL cases, 48% were pediatric (range, 2.9 to 18
years) and the remainder were adults (range, 18 to 73 years).
Median follow-up was 1.6 years (4.9 years for survivors). The
regimens used to treat BL were grouped into CHOP-like regimens
(CHOP (Fisher 1993), CNOP (Vose 2002)) or intensive regimens (BFM
(Pees 1992), CODOX-M VAC (Magrath 1996), and intensive chemotherapy
regimens combined with autologous stem cell transplant (ASCT)).
FISH for c-myc translocation was performed in 67 of the 71 cases,
including all cases in which BL was not ruled out by
immunohistochemistry or morphology, and 52 cases were found to be
positive. FISH for BCL2 translocation was performed in 44 of the 71
cases, with seven cases testing positive.
[0295] After pathological review and reclassification, the 71 cases
originally submitted as BL or Burkitt-like lymphoma were divided
into classic BL (25 cases), atypical BL (20 cases), DLBCL (20
cases), and high grade lymphomas that could not be classified by
current WHO criteria (six cases). This re-review diagnosis, which
is summarized in Table 2419, provided the standard against which
gene expression-based predictors were measured.
TABLE-US-00060 TABLE 2419 Submitting diagnosis Pathological
diagnosis Total cases Gene expression diagnosis Total cases BL or
Burkitt-like Classic BL 25 BL 25 lymphoma Atypical BL 20 BL 19 (71
cases) DLBCL 1 DLBCL 20 BL 7 DLBCL 13 High grade lymphoma (NOS) 6
DLBCL 5 BL 1 DLBCL (223 cases) DLBCL 223 ABC 78 GCB 82 PMBL 33
Unclassified DLBCL 30 High grade DLBCL DLBCL 9 ABC 6 (9 cases) GCB
2 BL 1
[0296] RNA was extracted from each of the 303 samples as described
previously (Alizadeh 2000). Gene expression profiling was performed
using the custom oligonucleotide Lymphoma microarray; which
contains oligonucleotides corresponding to 2,524 unique genes that
are differentially expressed among the various forms of
non-Hodgkin's lymphoma. The primary gene expression profiling data
is available at http://llmpp.nlh.gov/BL. A subset of the samples
were profiled on whole-genome Affymetrix U133 plus 2.0 arrays as
well.
[0297] To develop a gene expresslon-based diagnosis of BL, the
initial focus was on those cases that were submitted as BL and
confirmed as such by pathological review (45 cases). A set of genes
were identified that were differentially expressed between these BL
cases and each of the DLBCL subgroups (FIG. 35A). Pair-wise
Bayesian compound covariance predictors were constructed between BL
and ABC, BL and GCB, and BL and PMBL as described previously
(Rosenwald 2003a; Rosenwald 2003b; Wright 2003). For each
comparison of two lymphoma types, a linear predictor score was
calculated by:
LPS ( S ) = j t j S j , ##EQU00011##
where S.sub.j is the expression of gene j in a sample S and t.sub.j
is a scale factor representing the difference in expression of gene
j between a first lymphoma type and a second lymphoma type
(Radmacher 2002). The scale factor used was the t-statistic
generated by a t-test for the difference in expression between the
two subtypes being compared. Bayes' rule was then applied to the
distribution of the linear predictor scores to estimate the
probability that the sample was a member of either group. Each
comparison between BL and a DLBCL subtype proceeded in two stages
using different sets of genes to create a compound covariance
predictor as described above.
[0298] Stage one utilized c-myc and its target genes, which were
defined using an RNA interference experiment. For the RNA
interference experiment, the OCl-Ly10 DLBCL cell line was
transfected by electroporation (Amaxa Inc., Gaithersburg, Md.) with
small interfering RNAs (siRNAs) targeting the c-myc gene (Smart
pool; Dharmacon, Lafayette, Colo.). Gene expression in
RNAi-transduced OCl-Ly10 cells was compared to that of
control-transfected OCl-Ly10 cells using Lymphochip microarrays
(Alizadeh 1999). Genes that were at least 40% downregulated at 16
and 18 hours post-RNAi transfection and whose mRNA expression
levels were correlated with c-myc mRNA expression (r>0.4 across
all lymphoma samples) were defined as c-myc target genes (FIG.
35C). The majority of these genes have been previously described as
c-myc target genes (Zelfer 2003; Basso 2005). Stage two utilized
the 100 genes that exhibited the largest t-statistics
differentiating expression in BL from expression in each DLBCL
subtype, excluding genes used in stage one.
[0299] For a sample to be classified as BL, it had to be predicted
to be BL in both stages of the predictor in each of the three
pairwise comparisons between BL and the various DLBCL subtypes.
Leave-one-out cross-validation was used to evaluate the predictor
performance and minimize bias (Hills 1966; Ransohoff 2004; Mollnaro
2005).
[0300] Among the 25 cases identified as classic BL by pathological
review, the gene expression-based predictor classified 100%
correctly (FIG. 35B). Atypical BL and classic; BL could not be
distinguished by gene expression, and therefore the predictor also
classified 19 of the 20 atypical BL cases as BL. The cases for
which the gene expression-based and pathology-based diagnoses were
in agreement were labeled "BL-concordant" cases. The gene
expression-based predictor also exhibited 100% accuracy in the
diagnosis of ABC, GCB, and PMBL, and additionally classified all
but one of the unclassified DLBCLs as DLBCL (FIG. 35C).
[0301] In addition to leave-one-out cross-validation, the BL
prediction algorithm was tested by dividing the cases into equally
sized training and validation sets. The predictor was generated
using data from the training set and applied to the validation set
cases. This analysis agreed well with leave-one-out
cross-validation in 99% of the validation set cases, suggesting
that the predictive algorithm is highly effective in distinguishing
BL from DLBCL.
[0302] Having established the accuracy of the BL predictor, it was
next used to classify those 26 cases that were originally submitted
as BL or Burkitt-like lymphoma but were reassigned based on
pathological review as either DLBCL (n=20) or high grade lymphoma
not otherwise specified (NOS) (n=6). The expression-based predictor
disagreed with the pathological diagnosis in eight of these cases
(31%). In addition, the expression-based predictor classified one
of the nine cases submitted and verified as high-grade DLBCL as
BL.
[0303] Altogether, nine cases that were diagnosed as either DLBCL
or high grade lymphoma upon pathological review had gene expression
profiles consistent with BL. These cases were labeled
"BL-discrepant" cases (marked by an asterisk in FIG. 35D). The
BL-discrepant cases could be readily distinguished from all
subtypes of DLBCL by gene expression, and had an assigned
probability of being. BL ranging from 98% to 100% (FIG. 36A). The
diagnosis-of BL in the BL-discrepant cases was supported by the
presence of a c-myc translocation in all cases. Four of the nine
BL-discrepant cases expressed BCL2 mRNA and protein at high levels,
and three had a t(14:18) translocation involving the BCL2 gene in
addition to the t(B;14) translocation. The remaining five
BL-discrepant cases were BCL2-negative and completely
indistinguishable from BL by gene expression. In summary, although
the BL-discrepant cases did not meet the WHO criteria for a
diagnosis of BL based on morphology and immunophenotype, they
nonetheless harbored a c-myc translocation and were
indistinguishable from classic BL by gene expression.
[0304] It was next examined whether the expression-based BL
predictor could distinguish BL from DLBCL bearing a c-myc
translocation. Consistent with previous studies, 7% of the cases
submitted as DLBCL (six of the 87 cases tested) were found to have
a c-myc translocation. The gene expression profiles of these six
cases were distinct from those of BL (FIG. 36B). All six cases had
profiles of DLBCL (4 GCB, 2 ABC). Five of these cases had a BL
predictor probability of 0%, but one had a BL predictor probability
of 66% and may represent a rare biological overlap between BL and
DLBCL.
[0305] To elucidate biological mechanisms that distinguish BL from
DLBCL, hierarchical clustering (Eisen 1998) was used to organize
the BL predictor genes according to their expression patterns
across all BL and DLBCL samples. Many of the predictor genes
segregated into four gene expression signatures reflecting
distinctive biological attributes of BL. For example, c-myc and its
target genes constituted one gene expression signature, which was
more highly expressed in BL than in DLBCL, reflecting the influence
of the c-myc translocation in BL (FIG. 37A).
[0306] Another cluster of predictor genes that were more highly
expressed in BL than DLBCL included genes characteristically
expressed in normal GC B cells, such as MME (CD10) and MYBL1. This
was unexpected given that GCB, like BL, is derived from the
germinal center stage of B cell differentiation (Mann 1976;
Alizadeh 2000). To define a comprehensive GC B cell gene expression
signature, whole genome microarrays were used to profile gene
expression in various normal B cell subsets, including GC B cells,
as well as resting and nitogen-stimulated blood B cells. GC B cell
signature genes were defined as those that were overexpressed in GC
B cells compared with the blood B cell populations, but were not
associated with cellular proliferation. These GC B cell signature
genes could be divided into three sets; 1) genes that were
expressed more highly in BL than GCB ("BL-high"), 2) genes that
were expressed more highly expressed in GCB than BL ("BL-low"), and
3) genes that were expressed equivalently in BL and GCB (FIG. 37B).
Thus, BL and GCB retain expression of different subsets of GC B
cell signature genes.
[0307] A third gene expression signature included MHC class I genes
that were expressed at lower levels in BL than in DLBCL (FIG. 37C).
A fourth signature included known targets of the NF-.kappa.B
pathway that were expressed at relatively low levels in BL.
Expression of a recently defined set of NF-.kappa.B target genes
(Lam 2005) was examined, and it was found that BL expressed these
genes at very low levels compared to each DLBCL subgroup, including
GCB (FIG. 37D).
[0308] Expression was quantitated for each gene expression
signature within the various lymphoma types. For each signature,
the average expression of its component genes in a lymphoma biopsy
sample was calculated to generate a gene expression signature value
for that sample. FIG. 37E displays the signature values for
biopsies classified according to their molecular diagnoses.
BL-concordant samples had signature values that were readily
distinguished from those of samples belonging to the three DLBCL
subtypes (P<1.times.10.sup.-7). Notably, BL-discrepant samples
had signature values that were similar to those of BL-concordant
cases, again supporting classification as BL. The BL-discrepant
cases that were BCL2-negative (n=5) were indistinguishable from the
BL-concordant cases by gene expression. In contrast, the
BL-discrepant cases that were BCL2-positive (n=4) had lower
expression of the BL-high GC B cell gene expression signature. The
two BL-concordant cases with a t(14;18) also had low expression of
the BL-high gene expression signature. A final important
observation was that DLBCL samples with a c-myc translocation were
easily distinguishable from BL in the expression of all four gene
expression signatures (p<0.01).
[0309] To understand the effect of treatment on overall survival in
BL, clinical data was analyzed from patients with a molecular
diagnosis of BL for whom complete clinical information was
available. Overall survival was markedly better for patients who
received intensive chemotherapy regimens than for those who
received CHOP-like regimens (P=0.02; FIG. 38B). The inferior
outcome of adult patients treated with CHOP-like regimens could not
be accounted for by differences in age, stage, serum lactate
dehydrogenase, performance status, sites of disease, or the
presence of t(14;18). Among BL-discrepant cases, CHOP-like
therapies were also inferior (P=0.049), although the number of
cases is low (n=7; FIG. 38C). BL patients who received CHOP-like
regiments had a lower survival compared to patients in each of the
three DLBCL subtypes who received similar therapy (FIG. 38D).
Overall, these results are consistent with previous reports (Butler
1993; Magrath 1996; Smeland 2004) indicating that BL patients have
excellent-outcomes when treated with intensive chemotherapy
regimens rather than CHOP-like regimens.
Example 20
Identification and Characterization of Cyclin D1-Negative MCL
Cases
[0310] Lymph node biopsies from six patients with suspected cyclin
D1-negative MCL were examined. Two of these cases were identified
in a previous study (Rosenwald 2003a), and the other four were
newly identified as cyclin D1-negative MCL based on
immunohistochemistry and RT-PCR analysis. Each of these six cases
exhibited the characteristic morphological characteristics of MCL
as determined by a panel of expert hematopathologists.
[0311] Gene expression data was obtained using a Lymphochip
microarray and Affymetrix U133A/B microarrays, and the gene
expression profile of each case was compared to those of ABC (78
cases). GCB (85 cases), PMBL (33 cases), FL (193 cases), MALT (14
cases), splenic marginal zone lymphoma (SMZL) (6 cases), and SLL
(14 cases) (FIG. 33). The distributions of the Bayesian predictor
for each category were used to estimate the probability that any
particular sample belonged to that category by applying Bayes' rule
(Rosenwald 2003a; Wright 2003). Specifically, a Bayesian predictor
was generated for each lymphoma category between that category and
cyclin D1-positive MCL samples, based on the 50 genes with the
largest t-statistics between them. Only those samples for which all
pair-wise predictors agreed that there was a greater than 90%
probability that the sample was MCL were classified as cyclin
D1-negative MCL. This set of models was applied to the data set in
a leave-one-out cross-validated fashion so that the models tested
on a given sample were based on a data set that excluded that
sample. Samples that exhibited less than a 90% probability of
belonging to a category were deemed "unclassified." All six
suspected cyclin D1-negative MCL cases were indicated as MCL in all
pair-wise models with at least 99.99% confidence. None of the
samples from the other categories were indicated as MCL with
greater than 20% confidence in their respective pair-wise
comparisons. Thus, the six samples are considered to be bona fide
cases of cyclin D1-negative MCL.
[0312] Lymph node specimens from the six cyclin D1-negative MCL
cases were fixed in 10% neutral buffered formalin and embedded in
paraffin, and 4 .mu.m sections were cut and stained with
hematoxylin and eosin (H&E) for histologic evaluation.
Immunohistochemical stains for cyclin D1 protein were performed on
formalin-fixed, paraffin-embedded tissue sections. After
deparaffinization in xylene and rehydration in graded alcohols,
endogenous peroxidase was blocked with hydrogen peroxide.
Heat-induced antigen retrieval was performed using citrate buffer,
pH 6.0 (Brynes 1997). After rinsing in phosphate-buffered saline,
mouse anti-cyclin D1 antibody was applied at a dilution of 1:200
and rabbit monoclonal anti-cyclin antibody (SP4) (Neomarkers,
Fremont, Calif.) was applied using the suggested procedure for
antigen retrieval with minor modifications (Cheuk 2004) (Table
2416). Antibodies against CD3, CD5, CD20, CD23, CD43, cyclin D2,
cyclin D3, cyclin E, retinoblastoma protein (RB), and p27.sup.Klp1
were also employed for immunohistochemical stains (Table 2416).
TABLE-US-00061 TABLE 2416 Antibody Clone Source Dilution Retrieval
CD3 PS1 Ventana (Tucson, AZ) Neat A (10 mM citrate buffer, pH 6.0,
30 min., water bath (95.degree. C.)) CD5 4C7 Novocastra (Newcastle
upon 1:20 A Tyne, UK) CD20 L26 DAKO (Carpinteria, CA) 1:200 A CD23
BU38 The Binding Site (San Diego, CA) 1:5 B (Protease I enzymatic
digestion, 8 min.) CD43 L60 Ventana Neat None Cyclin D1 DCS-6 DAKO
1:200 A Cyclin D1 SP4 Neomarkers (Fremont, CA) 1:100 C (1 mM EDTA,
pH 8.0, 30 min., water bath (95.degree. C.)) Cyclin D2 Polyclonal
Santa Cruz Biotech (Santa Cruz, 1:500 D CA) (1 mM EDTA, pH 8.0, 60
min., water bath (95.degree. C.)) Cyclin D3 DCS-22 Neomarkers 1:100
E (10 mM citrate buffer, pH 6.0, 10 min., pressure cooker
(115.degree. C.)) Cyclin E 13A3 Novocastra 1:10 E RB Rb1 DAKO 1:10
A p27.sup.kip1 SX53G8 DAKO 1:20 A
[0313] Stains were performed on a Ventana ES automated
immunostainer (Ventana Biotek, Tucson, Ariz.) with a
streptavidin-biotin peroxidase detection system. Positivity for the
cycDns, RB, and p27.sup.Klp1 was defined as a strong nuclear
staining in more than 50% of the neoplastic cells. Results of
histologic and immunologic studies are set forth in Table 2417.
TABLE-US-00062 TABLE 2417 Case 1 2 3 4 5 6 Pathologic Growth
pattern Nodular Diffuse Nodular Diffuse Nodular Nodular features
Cytology Typical Typical Typical Typical Typical Typical CD20 + + +
+ + + CD3 - - - - - - CD5 + + + + + + CD23 - - - +(w) - - CD43 +(w)
+ - + + + Cyclin D1 - - - - - - Cyclin D2 + + - - - NA Cyclin D3 -
- + + + NA Cyclin E - - - - - NA RB + + + + + NA p27.sup.Kip1 - - -
- - - Genetic 1(11; 14)(q13; q32) - - - - - - features 11q13
(cyclin D1) Normal* Normal Normal Normal Normal Normal 12p13
(cyclin D2) Normal Normal Normal Normal Normal Normal 6p21 (cyclin
D3) Normal Normal Normal Normal Normal Normal 12p13 (p27.sup.Kip1)
Normal Normal Normal Normal Normal Normal NA: not available; +:
positive; +(w): weakly positive; -: negative; *normal indicates no
split or amplification
[0314] All six cases exhibited a nodular or diffuse growth pattern
and consisted of tumor cells with typical mantle cell cytology
(FIG. 34A). Immunophenotypic analysis of the tumor cells revealed a
B-cell phenotype in all cases. Expression of CD5 antigen was noted
in all six cases, white CD43 expression was observed in five of the
six cases. The tumor cells in one of the six cases were weakly
positive for CD23 antigen.
[0315] All six cases were negative for cyclin D1 using the mouse
monoclonal antibody DCS-6 (FIG. 34B). All four of the cases that
were tested using the rabbit monoclonal antibody SP4 were negative
for cyclin D1. Two cases (1 and 2) demonstrated overexpression of
cyclin D2 by Immunostaining (FIG. 34C), which correlated well with
the increased cyclin D2 mRNA levels detected by microarray analysis
(FIG. 33, lower panel). Both of these cases were negative for
cyclin D3. Three cases (3-5) exhibited overexpression of cyclin D3
by immunostaining (FIG. 34D), which correlated well with the
increased cyclin D3 mRNA levels detected by microarray analysis
(FIG. 33, lower panel). Case 6 also showed upregulation of cyclin
D3 mRNA by microarray analysis (FIG. 33, lower panel), but the
tissue block for this case was not available for
immunostaining.
[0316] All six cases were negative for cyclin E, but showed
positive immunostaining for RB. RB expression levels were similar
in all of the cases, and were comparable to those seen in cyclin
D1-positive MCL. Downregulation of p27.sup.Klp1 expression was
observed in all six cases, with the intensity of nuclear staining
much weaker than that seen in reactive T-lymphocytes.
[0317] Interphase FISH analysis was performed on cells left over
from prior cytogenetic analyses or on formalin-fixed,
paraffin-embedded tissue sections. For detection of the
t(11;14)(q13;q32), a commercially-available LSI IGH/CCND1
double-color, double-fusion probe was used (Vysls Inc., Downers
Grove, Ill.).
[0318] For break-apart FISH assays for the CCND1 (11q13), CCND2
(12p13), and GDKN1B/p27KlP1 (12p13) loci, appropriate BAC clones
flanking the respective genes were selected using bioinformatic
resources available from the University of California at Santa
Cruz. All BAC clones were derived from the RPCl11 library and were
obtained from Invitrogen/Research Genetics or the Sanger Center.
The following clones were used: CCND1 (pooled
RP11-211G23/RP11-378E8 and pooled RP11-30016/RP11-626H12), CCND2
(RP11-578L13 and RP11-388F6), and CDKN1B/p27KlP1(RP11-180M15 and
RP11-59H1). For each locus, centromeric and telomeric BAC clones
were differentially labeled with Spectrum Orange or Spectrum Green
(Vysis Inc.) and pooled for break-apart assays. Bacterial culture,
BAC DNA isolation and labeling, probe preparation, and FISH on
cytogenetic suspensions were performed as previously described
(Schlegelberger 1999; Martin-Subero 2002). The CCND3 locus was
investigated using a recently-described break-apart assay (Sonoki
2001). Locus-specific interphase FISH was performed on
paraffin-embedded tissue sections according to the manufacturer's
Instructions (Vysis Inc.), or recently-described protocols (Ye
2003) with minor modifications. Whenever possible, at least 100
cells were analyzed.
[0319] None of the six cases displayed the IGH/CCND1 fusion. FISH
studies with the locus-specific probe were also negative for
variant translocations or amplifications involving the CCND1 locus
at band 11q13 in ail six cases (Table 2417). Conventional
cytogenetic analysis was also performed on case 6, and did not
reveal a chromosomal alteration affecting band 11q13. FISH analysis
using break-apart probes for the CCND1 (12p13), CCND2 (6p21), and
CDKN1B/p27KP1 (12p13) loci did not reveal any evidence of
chromosomal translocation or amplification in these cases (Table
2417).
[0320] The lNK4a/ARF locus encodes the tumor suppressor proteins
p16.sup.INK4a and p14.sup.ARF. To detect genomic loss of the
INK4a/ARF tumor suppressor locus in the specimens, quantitative
real-time PCR assays were performed using genomic DNA as previously
described (Rosenwald 2003a). The REL locus on chromosome 2p was
chosen as the reference gene, and a cutoff ratio of INK4a/ARF locus
copy number relative to REL locus copy number was used to assess
tumor DNA for genomic deletions. A tumor DNA sample that yielded an
INK4a/ARF to REL ratio below the cutoff ratio was considered to
have a genomic deletion of the INK4a/ARF locus. The primers and
probe sets for the INK4a/ARF and the REL loci have been described
previously (Goff 2000; Labuhn 2001). No INK4A/ARF locus deletions
ware detected in any of the six cases.
[0321] Clinical features of the six patients are summarized in
Table 2418. The patients consisted of five males and one female
with a median age of 61 years (range, 54-77 years). All patients
presented with stage IV disease. Lymphadenopathy was the most
common presentation and extranodal sites were involved by lymphoma
in all six patients. Five patients received
combination-chemotherapy initially, but none of these patients
achieved a complete clinical response. One patient (case 1) was not
treated initially and developed gastrointestinal involvement 26
months after the initial diagnosis. At the time of last follow-up,
one of the patients had died and the other five were alive with
disease.
[0322] Ninety-three cases (92 cases in the original study plus the
false negative case) of cyclin D1-positive MCL (Rosenwald 2003a)
were used for comparison. The median follow-up for these patients
was 26 months (range, 7-166 months). The clinical features
including age and sex distribution, stags, presence of B symptoms,
serum lactate dehydrogenase (LDH) levels, extranodal sites, IPI
scores, types of treatment, and clinical responses were similar
between the cyclin D1-positive and cyclin D1-negative groups. At
the time of last follow-up, 65 of 93 patients with cyclin
D1-positive MCL had died, with a median overall survival of 31
months. No significant difference in overall survival was
identified between the cyclin D1-positive and cyclin D1-negative
groups.
TABLE-US-00063 TABLE 2418 Case 1 2 3 4 5 6 Age (years)/sex 54/F
61/M 61/M 60/M 54/M 77/M Ann Arbor stage IV IV IV IV IV IV B
symptoms - + - + - - Serum LDH levels Normal High Normal High
Normal Normal Extranodal sites BM, PB BM BM BM, spleen BM BM, lung,
GI IPI score 2 3 2 3 2 3 Initial therapy None R-CHOP CHOP COP CHOP
COP Response NA PR PR PR PR PR Progression + - + + + + Follow-up
(months) 38 5 88 19 70 30 Status AWD AWD DOD AWD AWD AWD LDH,
lactate dehydrogenase; BM, bone marrow; PB, peripheral blood; GI,
gastrointestinal tract; R, Rituxan; PR, partial response; AWD,
alive with disease; DOD, dead of disease
[0323] As stated above, the foregoing is merely intended to
illustrate various embodiments of the present invention. The
specific modifications discussed above are not to be construed as
limitations on the scope of the invention. It will be apparent to
one skilled in the art that various equivalents, changes, and
modifications may be made without departing from the scope of the
invention, and it is understood that such equivalent embodiments
are to be included herein. All references cited herein are
incorporated by reference as if fully set forth herein.
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